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Using Geochemical and Environmental Isotopic Tracers to Evaluate Groundwater Recharge and Mineralization Processes in Qena Basin, Eastern Nile Valley, Egypt
Using Geochemical and Environmental Isotopic Tracers to Evaluate Groundwater Recharge and...
Reda, Amira;Eissa, Mustafa;Shamy, Ibrahim El;Dotsika, Elissavet;Saied, Mostafa;Mosaad, Sayed
2022-08-23 00:00:00
applied sciences Article Using Geochemical and Environmental Isotopic Tracers to Evaluate Groundwater Recharge and Mineralization Processes in Qena Basin, Eastern Nile Valley, Egypt 1 1 , 2 , 3 4 1 3 Amira Reda , Mustafa Eissa *, Ibrahim El Shamy , Elissavet Dotsika , Mostafa Saied and Sayed Mosaad Desert Research Center, Division of Water Resources and Arid Land, Hydrogeochemistry Department, Cairo P.O. Box 11753, Egypt Center for Water Supply Studies, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA Faculty of Sciences, Geology Department, Helwan University, Helwan P.O. Box 11795, Egypt Stable Isotope Unit, National Centre for Scientific Research (N.C.S.R.) “Demokritos”, Institute of Nanoscience and Nanotechnology, Patriarchou Gregoriou (End) and Neapoleos Street, 15341 Agia Paraskevi, Greece * Correspondence: mustafa.eissa@drc.gov.eg Abstract: The Qena basin (16,000 km ) represents one of the largest dry valleys located in the arid Eastern Desert of Egypt. Groundwater resources in this watershed are scarce due to limited recharge from annual precipitation. Hydrogeochemistry and environmentally stable isotopes were utilized to determine the main sources of recharge and geochemical processes affecting groundwater quality. The studied basin comprises three main groundwater aquifers: the Quaternary aquifer, the Post-Nubian aquifer (PNA) of the Paleocene-Eocene age, and the Nubian Sandstone aquifer (NSA) of the Lower Cretaceous age. Groundwater types vary from fresh to brackish groundwater. The groundwater salinity of the Quaternary aquifer ranges from 426 to 9975 mg/L with an average of 3191 mg/L, the PNA’s groundwater salinity ranges from 1134 to 6969 mg/L with an average of 3760 mg/L, Citation: Reda, A.; Eissa, M.; Shamy, and the NSA’s groundwater salinity ranges from 1663 to 1737 mg/L with an average of 1692 mg/L. I.E.; Dotsika, E.; Saied, M.; Mosaad, S. The NSA’s groundwater is relatively depleted of stable isotopes’ signatures (ranges: O from Using Geochemical and 9‰ to 4.81‰; H from 71‰ to 33.22‰), whereas the Quaternary aquifer ’s groundwater is Environmental Isotopic Tracers to 18 2 relatively enriched (ranges: O from 5.51 to +4.70‰; H from 40.87 to +37.10‰). Geochemical Evaluate Groundwater Recharge and and isotopic investigations reveal that the NSA groundwater is a paleo-water recharged in a cooler Mineralization Processes in Qena climate. In contrast, the upstream Quaternary groundwater receives considerable recharge from Basin, Eastern Nile Valley, Egypt. recent meteoric water and upward leakage from the artesian NSA. The downstream Quaternary Appl. Sci. 2022, 12, 8391. https:// aquifer in the delta of the Qena basin is composed of original groundwater mixed with recharge doi.org/10.3390/app12178391 from the River Nile. Isotopic analysis confirms that the PNA’s groundwater recharge (ranges: Academic Editor: Valerio Comerci 18 2 O from 5.90 to 0.10; H 58.21 to 7.10‰) mainly originates from upward leakage from Received: 1 January 2022 the NSA under the artesian condition and seepage from the upper unconfined Quaternary aquifer. Accepted: 11 August 2022 NETPATH geochemical model results show that water–rock interaction, evaporation, and mixing are Published: 23 August 2022 the main geochemical and physical processes controlling the groundwater quality. NSA groundwater has a significant regional extension and salinity suitable for use in expanding agricultural projects; it Publisher’s Note: MDPI stays neutral should be well managed for sustainable development. with regard to jurisdictional claims in published maps and institutional affil- iations. Keywords: hydrogeochemistry; environmental isotopes; Qena basin; geochemical models Copyright: © 2022 by the authors. 1. Introduction Licensee MDPI, Basel, Switzerland. In arid regions, groundwater represents one of the primary sources of water for agri- This article is an open access article cultural and other development projects, especially in remote watersheds. Wadi Qena is distributed under the terms and located in the Eastern Desert of Egypt, draining toward the Nile valley. It is considered a conditions of the Creative Commons promising area for agricultural and sustainable development projects. Wadi Qena is bound Attribution (CC BY) license (https:// by the Nile River to the west and the Red Sea mountains series ridges to the East. The Wadi creativecommons.org/licenses/by/ flows from north to south, unlike other major Egyptian Nile drainage systems, which are 4.0/). Appl. Sci. 2022, 12, 8391. https://doi.org/10.3390/app12178391 https://www.mdpi.com/journal/applsci Appl. Sci. 2022, 12, 8391 2 of 21 generally oriented from east to west [1]; the Wadi covers an area of 16,000 km with an 0 0 average width of 75 km [2]. Wadi Qena lies between latitudes 26 15 00” N and 28 15 00” N 0 0 and between longitudes 32 15 00” E and 33 30 33” E (Figure 1). It is easily accessible through a road network, connecting the densely populated Nile Valley with the touristic 8 3 Red Sea Province. Wadi Qena receives 1.4 10 m annual precipitation, which feeds the aquifers [3]. In addition, it has mostly flatlands that are suitable for land development in downstream regions. Climatic data reveals that the maximum relative humidity varies from 53% in winter to 29% in summer. The average maximum temperature is approx- imately 23 C in winter and 44 C in summer, whereas the minimum is approximately 10 C in winter and 22 C in summer [4]. The average maximum recorded evaporation rate is 17.63 mm during June, whereas the average minimum recorded evaporation rate is 4.54 mm in December (Egyptian Meteorological Department 1935–2000). In the past decade, Wadi Qena has experienced rapid development, primarily related to agricultural projects that resulted in increased demand for groundwater resources. These groundwaters are exploited from three main aquifers: the Nubian Sandstone aquifer (NSA), the Post-Nubian carbonate aquifer (PNA), and the alluvial Quaternary aquifer [5,6]. Understanding the main processes controlling groundwater chemistry and recharge is important for sustainable management of groundwater resources used in this arid wa- tershed. In this respect, gathering information related to recharge mechanisms, geochemi- cal characteristics, and groundwater evolution is necessary for sustainable groundwater use [7–9]. Variations in groundwater geochemistry within the aquifers result from salt leaching in the aquifer matrix, cation exchange processes, and the length of time the ground- water remains in the aquifer [10]. However, local geology, the degree of rock weathering, the quality of recharge water, and inputs from sources other than rock–water interaction can influence groundwater chemistry throughout its flow path [11–13]. Moreover, accu- rately identifying the groundwater recharge mechanism and its sources using conventional hydrogeological methods is difficult [7,8,14]. In arid regions, integrating these methods with geochemical and environmental isotopic tracers can be utilized to understand the geochemistry of the groundwater, recharge sources, and to determine evolutionary pro- cesses [9,15]. It can also provide relevant information regarding the origin of groundwater mineralization [16]. Geochemical indicators and environmental isotopes offer unique and valuable insights regarding the origin of groundwater and its movements. They can also be used to effectively characterize tracing of contaminants and solute transport in ground- water [17]. They allow quantitative evaluation of mixing and other physical processes such as evaporation and isotopic exchange in hydrogeologic systems [18]. These integrations have been applied in many arid areas, including Australia, China, Tunisia, Saudi Arabia, and Egypt [15–17,19–22]. The main goal of this study is to utilize hydrogeochemical data and isotopic tracers, in addition to geochemical modeling, to (1) assess the geochemical processes controlling groundwater evolution, (2) investigate recharge sources and hydrogeochemical relations between the three principal groundwater aquifers, and (3) identify the mineralization sources that deteriorate groundwater quality. Appl. Sci. 2022, 12, 8391 3 of 21 Figure 1. Location of groundwater samples. Samples 1 to 48 were collected in November 2018; samples 49 to 104 were collected later [21,22]. 2. Geomorphology, Geology, and Hydrogeology The study area comprises three main geomorphologic units (Figure 2): mountains, plateaus, and depressions [5,23,24]. The Red Sea mountainous terrains are located in the east and are composed mainly of igneous and metamorphic rocks. The plateaus consist of El Maaza limestone and El Ababda sandstone highlands. The limestone plateau occupies the western portion of the studied basin, and the sandstone plateau breaks up into low ridges and isolated hills [25]. The characteristics of these elevated areas have notable impacts on the hydrogeologic setting [23,24]. The morphotectonic depression represents one of the most noticeable topographical features in the basin, a wide lowland that extends from the northern portion of Wadi Qena to the north of the Qena-Safaga road, linking the Qena district with the Red Sea coast. The Qena basin stratigraphy is composed of Precambrian (igneous and metamorphic) rocks overlain by Cretaceous to Quaternary sedimentary successions (Figure 2). The stratigraphic sequence consists of rock units [1,26–31] arranged from base to top as indicated in Figure 2: (1) Cretaceous, represented by Wadi Qena, Galala, Umm Omeiyied, Abu Aggag, Hawashiya, Quseir variegated shale, Duwi, Rakhiyat, and Sudr formations; (2) Paleocene, represented by Dakhla, Tarawan, and Esna formations; (3) Early Eocene, represented by the Thebes formation, and (4) undifferentiated Pliocene deposits beside the alluvial Quaternary sediments. The Wadi Qena basin was affected by shear faults, folds, and fractures, which are attributed to the Pan African orogeny and a series of tectonic reactivations, mostly during the Cretaceous and Oligocene eras [32–35]. Appl. Sci. 2022, 12, 8391 4 of 21 Figure 2. Wadi Qena geological map [36]. The groundwater is exploited from the Quaternary aquifer, the PNA, and the NSA (Aggour 1997 [5]). The Quaternary aquifer at Wadi Qena is the main groundwater source for irrigation; it is composed of gravel, coarse to fine sand, and conglomerates; its thickness increases downstream, attaining approximately 100 m (Figure 3; [5,37,38]. The aquifer is characterized by unconfined conditions; the water depth ranges from 1.9 to 20 m (Table 1), the maximum penetration depth from the ground surface elevation is 28 m, and the groundwater generally flows from northeast to southwest [25]. The Post-Nubian aquifer (PNA) contains water bearing limestones and sandstones of the Pliocene and/or Eocene ages. The groundwater is characterized by free water table conditions, the depth to groundwater level (DTW) ranges from 28 to 76 m, and the maximum groundwater well total depth (TD) is 200 m (Table 1). Figure 3 shows that the PNA aquifer is directly overlain by the Quaternary aquifer, where it is not separated by a confining layer of shale or clay sheets. Hence, mixing may occur naturally or be induced by pumping, affecting the groundwater chemistry. The NSA is formed mainly of sandstone intercalated with shale interbeds of the lower cretaceous age, and is considered one of the primary groundwater sources. The groundwater in the NSA is confined by impervious Quseir variegated shale overlying the aquifer [5]. The groundwater flows from northeast to southwest [25]. Appl. Sci. 2022, 12, 8391 5 of 21 Table 1. Hydrogeological parameters and geochemical analyses of groundwater samples collected from the Qena basin during the November 2018 field trip. TDS Ca Mg Na K CO HCO SO Cl Si NO 3 3 4 3 DTW TD Temp Aquifer pH No. DO (m) (m) ( C) mg/L 5 Quaternary 6.8 2.5 4 24.1 2.85 2716 123 35 760 36 0 177 850 824 12.5 9.80 7 Quaternary 7.2 3 4 25 2.13 8564 478 290 2150 47 0 195 1926 3574 9.8 12.60 9 Quaternary 7.8 3 6 22.6 3.24 3059 96 58 960 24 18 226 475 1316 11.2 11.20 11 Quaternary 7.4 4 5 24.5 3.4 7593 517 290 1750 23 0 98 1985 2979 15.6 14.00 12 Quaternary 7.6 – – 25.7 3.14 6226 517 242 1350 23 6 67 1423 2631 8.2 12.60 13 Quaternary 7.1 5 6.5 27.5 2.4 9976 776 315 2400 22 0 92 1556 4862 15.3 12.60 14 Quaternary 7.1 4 6 27.5 2.45 3849 484 116 700 11 0 79 960 1539 16.1 9.80 15 Quaternary 7.2 5.5 7 28.9 3.17 4214 458 162 780 14 0 67 1105 1662 12.4 7.00 16 Quaternary 7.2 – – 28 3.17 2703 319 92 480 9 0 61 790 983 8.5 4.20 17 Quaternary 7.8 20 – 32.3 0.45 1111 26 9 380 9 12 195 180 397 6.7 5.60 18 Quaternary 7.4 – – 26 2.9 2790 331 100 500 9 0 73 811 1003 9.3 8.40 19 Quaternary 7.3 – – 30.5 2.79 2138 269 58 400 8 0 55 591 784 11.1 9.80 25 Quaternary 7.1 6 8 27.3 2.45 5631 657 140 1150 15 0 92 1141 2482 15.8 12.60 27 Quaternary 7.5 6 28 21 2.9 2117 172 64 480 14 12 140 541 765 9.1 9.80 28 Quaternary 7.6 – – 21 1.2 427 51 24 64 16 12 244 63 74 14.1 11.20 29 Quaternary 7.1 17.5 – 27.1 0.9 4650 299 66 1300 31 0 31 835 2104 6.3 9.80 31 Quaternary 7 3 6 25.2 1 2148 249 82 360 17 0 287 830 467 25.8 12.60 32 Quaternary 7.3 6 7 24.4 1.59 849 86 39 155 9 12 183 278 179 16.5 19.60 33 Quaternary 7.2 1.9 – 22.4 2.9 1492 147 63 270 9 0 397 606 199 23.3 8.40 34 Quaternary 7.2 3.6 – 26 1.5 1030 97 52 190 8 0 305 333 199 21.8 7.00 35 Quaternary 7.2 – – 25.2 1.59 933 80 39 200 7 0 275 230 238 19.3 4.20 36 Quaternary 7 – – 26.5 1.9 2473 221 75 520 14 0 451 892 526 26.7 7.00 37 Quaternary 7.1 – – 25.5 1.53 914 67 60 170 9 0 329 320 124 23.8 4.20 40 Quaternary 8.3 – – 4.4 1607 90 66 380 8 18 79 479 526 18.9 0.00 41 Quaternary 7.3 – – 25.6 2.6 3523 367 104 700 14 0 226 1208 1018 30.3 5.60 42 Quaternary 8.6 – – – 7.8 5705 598 194 1100 21 12 37 1678 2085 15.4 19.60 43 Quaternary 7.9 – – – 4.13 2978 289 140 540 13 18 110 830 1092 20.8 0.00 44 Quaternary 8.1 – – – 4.4 1586 188 58 270 12 18 146 540 427 6.3 2.80 45 Quaternary 7.3 – – 25.1 2.6 2280 159 92 480 21 0 256 834 566 8.4 12.60 46 Quaternary 7.1 – – – – 2170 326 90 260 7 0 120 888 539 9.3 47 Quaternary 7.3 1485 175 42 256 5 0 72 650 322 10.3 1 P-Nubian 7.1 76 – 25 3.54 6969 438 242 1700 18 0 85 1450 3078 14.7 8.40 2 P-Nubian 7.1 30 72 24.2 1.91 5871 528 194 1300 31 0 116 1227 2534 12.5 33.60 3 P-Nubian 7.1 70 125 30.1 1.8 5649 518 179 1250 23 0 92 1200 2433 12.2 12.60 6 P-Nubian 7.2 51 95 29.1 1.82 6707 319 266 1700 29 0 140 1490 2833 11.3 11.20 10 P-Nubian 7.2 40 110 29.7 3.31 4152 418 133 860 15 0 73 1051 1638 13.6 5.60 20 P-Nubian 7.2 48 160 29.9 1.3 1299 147 31 260 7 0 92 361 447 12.9 9.80 21 P-Nubian 7.1 50 200 24.2 3.1 1478 183 36 300 10 0 85 300 606 9.8 8.40 22 P-Nubian 8 60 170 22.9 3.9 1353 157 41 270 10 6 61 361 477 11.4 4.20 23 P-Nubian 6.7 28 115 28.1 1.59 1339 78 32 350 7 0 79 356 477 7.9 5.60 26 P-Nubian 7.4 35 75 – 2.83 4546 462 145 950 17 0 67 1151 1787 11.5 4.20 38 P-Nubian 8.1 47 90 – – 1134 88 59 210 13 12 104 475 226 15.7 2.80 39 P-Nubian 7.6 40 70 26.8 3 4624 345 175 1050 16 0 92 1106 1887 15.5 16.80 4 Nubian 7.6 Flowing 800 44.4 0 1663 30 10 590 8 12 203 206 706 9.6 8.40 8 Nubian 8.2 Flowing 650 35.6 0 1737 31 11 610 19 18 165 141 826 9.5 8.40 24 Nubian 7.9 2 620 40 3 1676 92 27 470 21 12 116 430 566 9.0 7.00 30 Surface (Nile) 7.9 5 21.5 2.7 182 26 11 20 7 6 104 46 15 4.1 5.60 48 Canal Water 8 – – – – 1350 87 62 335 4 5 223 406 417 6.3 – Note: DTW is depth to groundwater level (m); TD is total depth of groundwater well (m); DO is dissolved oxygen; and Canal Water refers to a surface water sample collected from a subchannel from the River Nile. Appl. Sci. 2022, 12, 8391 6 of 21 Figure 3. N-S hydrogeological cross-section along traverse A-A’ of Figure 1, based on subsurface lithological data modified from [24,37]. 3. Methodology Water samples were collected from 48 wells (Table 1) in November 2018; Figure 1 shows the well location map of the study area. Samples were collected in polyethylene bottles for geochemical and isotopic analyses. pH and electrical conductivity (EC) were measured in the field. Electrical conductivity was measured using AD-410 ADWA testers; pH was mea- sured using the AD-11 ADWA model; testers were calibrated twice daily during the field campaign. Dissolved major-ion analyses, including anions (Cl, SO , and HCO ) and cations 4 3 (Ca, Mg, Na, and K), were conducted at the Desert Research Center, Water Central Labora- tory, Cairo, Egypt. Total dissolved solids (TDS) were estimated using the calculation method. Major cations and anions were analyzed in groundwater samples according to [39,40]. Carbonate (CO ) and bicarbonate (HCO ) levels were determined via titration against 3 3 H SO using the neutralization method, using phenolphthalein as an indicator for CO 2 4 3 and methyl orange as an indicator for HCO . Chloride (Cl ) levels were determined vol- 2+ umetrically via titration against AgNO using K CrO as an indicator. Calcium (Ca ) and 3 2 4 2+ magnesium (Mg ) levels were determined via titration against Na EDTA using a complex metric method. Calcium levels were determined using a murexide indicator; magnesium 2+ 2+ levels were estimated by subtracting the calcium values from the (Ca + Mg ) values after determining them using Eriochrome Black T in the presence of a suitable buffer solution. A Flame Photometer (PFP 7, Jenway, London, UK) was used to determine sodium (Na ) and + 2 potassium (K ) levels. Sulfate (SO ) levels were determined using the turbidity method using a UV/Visible Spectrophotometer, Unicam UV 300 (Thermo Spectronic, Waltham, MA, USA). The calculated e Error% = [å Cations å Anions]/[ å Cations + å Anions] was less than 5%. 18 2 Stable isotopic analyses for O and H were analyzed at the Stable Isotope and Radiocarbon Units, Institute of Nanoscience and Nanotechnology (INN), National Centre for Scientific Research “Demokritos” on a continuous flow Finnigan DELTA V plus equipped with a Gas bench device (Thermo Electron Corporation, Bremen, Germany) stable isotope mass spectrometer. Results are expressed in the standard notation, delta per mil (‰), for 18 2 both Oxygen ( O) and deuterium ( H). Appl. Sci. 2022, 12, 8391 7 of 21 Data obtained from the chemical analyses were used as input data for NETPATHXL [41] inverse geochemical modeling. NETPATHXL is a computer program that uses inverse geochemical modeling techniques to calculate net geochemical reactions that can account for changes in water chemistry between initial and final evolutionary waters along the flow path [15,42]. 4. Results 4.1. Groundwater Chemistry The chemical characteristics of the groundwater in the studied aquifers are presented in Table 1. According to the results of the chemical analyses, the pH of Quaternary aquifer groundwater ranged from 6.8 to 8.6 with a median of 7.3, the pH of PNA samples ranged from 6.7 to 8.1 with a median of 7.2, and the pH of NSA samples ranged from 7.6 to 8.2 with a median of 7.9. The pH values reflect that most groundwater samples had neutral to slightly alkaline characteristics. Groundwater temperature mainly depends on the geothermal gradient and ambient temperature at the land surface [43]. The groundwater temperature in the Quaternary aquifer ranged from 21 to 32.3 C, the PNA samples’ temperatures ranged from 22.9 C to 30.1 C, and the NSA samples’ temperatures ranged from 35.6 C to 44.4 C (Figure 4a). The total dissolved solids (TDS) measurement is usually used as a general indicator of water quality [44]. Groundwater is classified as a fresh, brackish, and saline [45]. Results (Table 1) show that the Quaternary groundwater ’s TDS measurements ranged from 426 to 9975 mg/L with a median value of 2472.6 mg/L, identifying it as a fresh to saline water type. The PNA samples’ TDS measurements ranged from 1134 to 6969 mg/L with a median of 4348.9 mg/L, identifying it as a fresh to saline water type. The NSA samples’ TDS measurements ranged from 1496 to 1737 mg/L with a median value of 1676 mg/L, identifying it as brackish water (Figure 4b). In the upper region of the analyzed area the Quaternary and PNA groundwater had lower TDS values (Figure 1) which may be attributed to the direct recharge from local precipitation. In addition, the Quaternary groundwater downward, close to the River Nile, had lower TDS values, indicating that + 2+ the River Nile percolates into the aquifer. In general, most of the major ions (Na , Mg , 2+ 2 Ca , SO , and Cl ) were positively correlated with TDS (Figure 5a–f), indicating that their concentrations’ increase was controlled by flow path, geochemical processes, and water–rock interaction between the groundwater and aquifer matrix. Figure 4. Box plot for the (a) temperature ( C) and (b) TDS (mg/L) of groundwater in the Wadi Qena basin. Appl. Sci. 2022, 12, 8391 8 of 21 Figure 5. Cont. Appl. Sci. 2022, 12, 8391 9 of 21 Figure 5. Major ions concentrations (mg/L) versus total dissolved solids (TDS) in mg/L relationships 2+ 2+ for groundwater wells tapping aquifers in the Qena basin (a) Ca Versus TDS, (b) Mg versus TDS, + + 2 (c) Na +K versus TDS, (d) HCO versus TDS, (e) Cl versus TDS, and (f) SO versus TDS. 3 4 Appl. Sci. 2022, 12, 8391 10 of 21 4.2. Chemical Water Types The major ion chemistry is shown by Piper ’s tri-linear diagram (Figure 6; [46]), which provides information regarding hydrogeochemical facies and the evolution of groundwater based on the relative proportions of major ions [47]. In the lower left triangle of the Piper diagram, groundwater samples from different aquifers are plotted between the two end members of the NSA groundwater and the surface water (Nile water and canal water). In the lower right triangle, groundwater samples from the NSA and PNA are shown to have higher Cl contents. In the diamond diagram, most of the three aquifer groundwater samples are distributed in subareas 7 and 9. Approximately 52% of the Quaternary groundwater samples, 100% of the PNA and NSA groundwater samples, and all canal samples are plotted in subarea 7, reflecting that Na and Ca are dominant cations, and that Cl and SO are dominant anions. In subarea 7, PNA samples are plotted in the upper corner of the diamond; NSA samples are plotted in the right side corner, due to variations in groundwater chemistry as a result of leaching and dissolution of diverse minerals rich in chloride that are embedded and form different aquifer matrices. In contrast, 32.26% of Quaternary groundwater samples are in subarea (9), where no cation–anion pair exceeds 50%, reflecting the impact of the mixing process due to drainage water infiltration. Figure 6. Piper diagram [46] showing the major ion water types of all water samples. Chemistry of the rainwater sample [48]. 4.3. Environmental Isotopes 18 2 Oxygen O and hydrogen H are ideal tracer isotopes that can be used to determine groundwater recharge and mixing sources. They form part of a water molecule that does not contribute to geochemical reactions; therefore, they provide good insights into the physical processes affecting groundwater, such as groundwater mixing and evaporation [49,50]. Based on isotopic data from groundwater samples collected in November 2018 and other historical records [23,24,51], isotope analysis results show that Oxygen O in Quaternary groundwater ranged from 5.51‰ (well 54) to +4.7‰ (well 28), from 5.9 ‰ (well 26) Appl. Sci. 2022, 12, 8391 11 of 21 to +4.9‰ (well 38) in PNA groundwater, and from 9 ‰ (well 4) to 4.81 ‰ (well 103) in NSA groundwater. The hydrogen H isotopes in the Quaternary aquifer ranged from 40.87 ‰ (well 54) to 37‰ (well 32), from 58‰ (well 26) to 43‰ (well 38) in the PNA, 18 2 and from 71‰ (well 4) to 33.22‰ (well 93) in the NSA. The O– H relationship (Figure 7a and Table 2) shows that most groundwater samples fell close to the global meteoric water line (GMWL, [52]), indicating that they were mainly of meteoric origin. 18 2 18 Figure 7. (a) O (‰) versus H (‰) and Cl (mg/L) (b) O (‰) versus Cl (mg/L) for ground- water samples tapping different aquifers in the Qena Basin, (GMWL, from [51]). Isotopic data serials greater than 48 are from [23,24,51]; the rainwater sample is from [53]. Appl. Sci. 2022, 12, 8391 12 of 21 Table 2. Recent and historical isotopic record data for chloride concentration (ppm), O (‰), and H (‰). 18 2 18 2 18 2 Cl O H Cl O H Cl O H No. Aquifer No. Aquifer No. Aquifer ppm (‰) ppm (‰) (‰) ppm (‰) 28 * Quaternary 74 4.7 36 64 Quaternary 1692 3.27 26.36 94 Nubian 566 6.66 49.59 29 * Quaternary 2104 0.2 4 65 Quaternary 1719 2.64 23.86 95 Nubian 590 6.95 52.33 32 * Quaternary 179 4.3 37 66 Quaternary 1859 4.44 34.81 96 Nubian 580 6.87 47.65 36 * Quaternary 526 4.1 31 67 Quaternary 1689 4.04 34.74 97 Nubian 669 6.39 49.74 42 * Quaternary 2085 3.6 26 68 Quaternary 1902 3.79 34.19 98 Nubian 665 6.74 50.92 44 * Quaternary 427 0.3 2 69 Quaternary 2667 3.92 33.36 99 Nubian 617 6.39 48.21 45 * Quaternary 566 1.6 18 70 Quaternary 3407 2.73 29.55 100 Nubian 640 5.26 38.17 1 * P-Nubian 3078 4.9 52 71 Quaternary 2654 3.72 32.79 101 Nubian 541 5.05 38.54 10 * P-Nubian 1638 5.6 56 72 Quaternary 8783 2.06 27.52 102 Nubian 377 4.82 33.28 21 * P-Nubian 606 5.8 57 73 Quaternary 2445 4.08 33.49 103 Nubian 621 4.81 35.24 26 * P-Nubian 1787 5.9 58 74 Quaternary 5355 0.58 19.59 104 Nubian 869 6.72 52.46 38 * P-Nubian 226 4.9 43 75 Quaternary 4845 3.43 32.88 105 Quaternary 655 0.8 11.2 39 * P-Nubian 1887 0.1 7 76 Quaternary 4095 3.04 30.07 106 Quaternary 50 3.7 23.3 4 * Nubian 706 9 71 77 Quaternary 1844 1.89 30.24 107 Quaternary 46 3.6 22.5 24 * Nubian 566 7.3 62 78 Quaternary 1437 4.55 38.68 108 Quaternary 822 0.3 14.4 49 Quaternary 541 4.45 32.73 79 Quaternary 2173 3.8 32.61 109 Quaternary 1287 1 6.5 50 Quaternary 412 3.6 23.5 80 Quaternary 3132 4.02 34.55 110 Quaternary 851 0.2 6.9 51 Quaternary 173 4.64 33.85 81 Quaternary 2109 4.34 35.97 111 Quaternary 1158 1.9 25.3 52 Quaternary 420 4.87 32.34 82 Quaternary 3481 4.26 37.78 112 Quaternary 1280 0.9 13.7 53 Quaternary 413 4.69 30.87 83 Quaternary 3807 1.4 25.22 113 Quaternary 2580 1.4 14.8 54 Quaternary 464 5.51 40.87 84 P-Nubian 1988 4.12 33.34 114 Quaternary 601 3.4 28.4 55 Quaternary 592 4.9 24.78 85 P-Nubian 2269 4.38 34.82 115 Quaternary 531 1.4 22.5 56 Quaternary 605 5.48 33.15 86 P-Nubian 3279 4.11 37.11 116 Quaternary 1230 3.2 25.1 57 Quaternary 654 4.79 34.46 87 P-Nubian 2175 4.6 37.22 117 Quaternary 385 1.3 10.8 58 Quaternary 1390 4.81 37.3 88 P-Nubian 5323 3.78 33.37 118 Quaternary 525 0.4 9.2 59 Quaternary 1268 4.81 35.95 89 P-Nubian 1318 4.51 36.67 119 Quaternary 1300 1.1 11.1 60 Quaternary 1355 5.16 38.27 90 P-Nubian 2632 3.81 33.7 120 Quaternary 616 2.6 19.5 61 Quaternary 1348 5.05 40.28 91 P-Nubian 826 4.69 37.72 121 Canal Water 80 3 34.1 62 Quaternary 2110 4.72 37.63 92 Nubian 648 7.07 48.67 122 Canal Water 80 3.2 34 63 Quaternary 2142 3.08 25.89 93 Nubian 636 5.77 33.22 123 Canal Water 80 3.3 24.3 Note: Isotopic data marked with an asterisk (*) are samples collected in November 2018; other data are from [23,24,51]. Canal Water refers to a surface water sample collected from a subchannel from the River Nile. 5. Discussion The current study attempts to utilize geochemical and environmental isotopic tracers to understand the geochemistry of groundwater and recharge sources to determine evolu- tionary processes in the Qena Basin, Eastern Nile Valley, Egypt. Integrating isotopic tracers with conventional hydrogeological methods can lead to relevant information regarding the origin of groundwater mineralization [16]. 5.1. Geochemical Processes Affecting Groundwater + 2+ 2+ 2 The results above show that most of the major ions (Na , Mg , Ca , SO , and Cl ) directly correlated with TDS (Figure 5a–f), indicating that increases in their concentrations were consistent with the flow path from upstream (northeast) to downstream (southwest) (Figure 1). Both geochemical and physical processes (dissolution and evaporation) as well as water–rock interaction were controlling factors for salinity variations in the study + + + + +2 area (Figure 8; [54]). Figure 8 represents the ratios of ((Na + K )/Na + K + Ca ) and major anions (Cl /Cl + HCO ) separately, as a function of TDS. The plot indicates that groundwater samples of the studied aquifers were primarily distributed in the evaporation dominance field. This suggests that the groundwater chemistry in the area was primarily controlled by the evaporation process, as well as the water–rock interaction factor, because the annual rainfall and groundwater recharge were insignificant. Appl. Sci. 2022, 12, 8391 13 of 21 Figure 8. Gibbs’s diagram with all water samples represents ratios of Na/(Na + Ca) and Cl/(Cl + HCO ) as a function of TDS. The chemistry of the rainwater sample is from [48]. The influence of hydrochemical processes that affect water quality such as ion ex- change, mixing, and leaching can be detected using chemical ion ratios [55–57]. In the current study, the relations between different ionic concentrations were used to understand the relationships between the ions and factors affecting groundwater chemistry (Figure 9). A higher concentration of sodium in the groundwater of the NSA and a lower concen- tration in the groundwater of the PNA indicate silicate weathering [58]. In contrast, the groundwater in the Quaternary aquifer and in most of the PNA samples showed a slightly lower concentration of Na , which may be attributed to the Ca/Na exchange process +2 + (Figure 9a) due to the presence of clay interbeds in the aquifers. The relations of Ca /Na versus HCO /Na (Figure 9b) show that most of the groundwater samples of the three + +2 +2, aquifers had more Na than Ca , Mg and HCO , which could be explained by silicate weathering. The relation of (Cl Na )/Cl vs. TDS (Figure 9c) shows that 51.61% of Quaternary samples and 83.33% of Post-Nubian samples in the study area had a positive + + value; this indicates a direct cation exchange process between Na and K dissolved in 2+ 2+ groundwater with Ca and Mg embedded in the aquifer matrix. In contrast, the rest of the Quaternary samples, the Post-Nubian samples and all Nubian groundwater samples had negative values that indicate a reverse cation exchange process. Appl. Sci. 2022, 12, 8391 14 of 21 Figure 9. (a) Cl Na, (b) HCO /Na versus Ca/Na, and (c) TDS/(Cl Na)/Cl relationships. Plots show different ionic relationships for groundwater wells tapping the three aquifers in the Qena basin. 5.2. Groundwater Recharge Mechanism The hydrogeologic setting in the study area indicates that groundwater within the studied aquifers is generally flowing from the northeast to the southwest [5,25]. Moreover, extensive structural deformation by dextral faults trending northeast to southwest and northwest to southeast controls the water-bearing horizons in the subsurface [23,24]. Data 18 2 for the stable isotopes Oxygen O and hydrogen H indicate that groundwaters from the different aquifers were primarily of meteoric origin (Figure 7a). Upstream Quaternary groundwater samples were relatively enriched with isotopic content and plotted close to the recent rainwater and the canal samples, confirming recharge from recent meteoric precipitation. Downstream groundwater samples located in the delta of the Qena basin were plotted close to the canal samples, indicating mixing with current recharge from Appl. Sci. 2022, 12, 8391 15 of 21 Nile water. In contrast, NSA groundwater was relatively depleted of isotopic content compared to other groundwater samples (Quaternay and PNA) and the recent rainfall isotopic signature, which confirms a paleo-water that had been recharged in a cooler climate. The Post-Nubian groundwater samples were plotted between the Nubian and the upstream Quaternary groundwater samples. Post-Nubian aquifer groundwater originated primarily from the upward leakage from the NSA under artesian conditions and seepage from the upper unconfined Quaternary aquifer. Moreover, the relationship between O and Cl (Figure 7b, Table 2) shows that upstream Quaternary groundwater samples were plotted between the most depleted Nubian groundwater samples, represented by well site 4 and the rainwater sample, indicating mixing due to percolation from the QA and upward infiltration from the NSA. Downstream Quaternary groundwaters were plotted close to the canal water, indicating promising recharge due to canal water seepage. Post- Nubian and Quaternary groundwater samples plotted on the right side had high dissolved chloride concentrations, probably due to leaching and dissolution of the aquifer matrix and evaporation processes. 5.3. Water–Rock Interaction and Mixing Model Chemical data from the groundwater samples and isotopic data were used in the NETPATH Model to estimate geochemical reaction and mixing with other sources [15,50]. This model estimates net geochemical reactions and observed variations in groundwater chemistry between initial and final groundwater wells along the groundwater subsurface flow path. However, this approach is limited by the input data related to the subsurface groundwater aquifer [59]. In this study, the NETPATH geochemical model is constrained by major dissolved ions in the groundwater including carbon (carbonate and bicarbonate ions) sulfur (to represent sulfate anions), calcium, magnesium, sodium, chloride, and silica (Table 3). Table 3. Constraints, phases, and processes used in NETPATH models. Constraints Phases Processes Albite, Alunite, Calcite, Chlorite, () Dolomite, Calcium, Carbon, Magnesium, ( ) Ca-Montmorillonite, Reaction and/or Evaporation Potassium, Sodium, Sulfur, K-Mica, Illite, Gypsum, Sio , and Mixing Chloride, Silica (+) Halite NaCl, ( ) Anorthite, () Exchange Note: () Dissolution and precipitation, (+) dissolution only, and ( ) precipitation only. The essential minerals embedded in the aquifer sediment were used as input phases to represent the interaction and hydrolysis between the groundwater and aquifer matrix. Calcite, dolomite, and halite minerals dominate terrestrial alluvial deposits (Quaternary aquifer) and the Post-Nubian carbonate aquifer. Gypsum, montmorillonite, and illite are dominant in the clay sheet intercalations of the Quaternary aquifer and the impervious Quseir variegated shale overlying the NSA [1]. Anorthite, alunite, and chlorite are used to simulate the basement aquifer and the main watershed area of the Qena basin. The Qena watershed is in Egypt’s arid zone; therefore, the evaporation parameter was selected to simulate the impact of aridity and scarce rainfall on groundwater salinization. A mixing parameter was used to simulate the possibility of recharge from the River Nile and mutual leakage from the multiple aquifer hydrologic system (confined, unconfined, and semi-confined). The model results show two main factors controlling the groundwater geochemistry: water–rock interaction and mixing models (Table 4). Appl. Sci. 2022, 12, 8391 16 of 21 Table 4. NETPATH water–rock interaction and mixing model results (mmol/L) representing groundwater in the Qena Watershed. Mixing Percent Phases Precipitated or Dissolved Initial Initial Final Aquifer Model Water-1 Water-2 Water Initial Initial Cal Dol Gyp Hal Si Ilt Chrt Mont Albt An Mic Alun Ex Ev Water-1 Water-2 54 None 55 – – 2.41 1.89 0.31 4.85 6.66 – 0.35 – 2.58 – – 0.01 – – 54 None 57 – – – – 1.79 5.78 9.48 – 0.37 – 2.69 1.26 – – 1.04 Quaternary 54 None 58 – – 10.4 6.08 1.73 27.51 9.36 – – 3.12 – – 0.41 – – aquifer 57 None 59 – – 3.29 – 9.64 17.44 22.83 – 0.47 – 8.08 – – – 7.36 – Reaction (Upstream) Models 59 None 66 – – – 2.38 3.36 12.83 – – 0.83 – – 1.25 – – 6.00 1.08 66 None 71 – – 3 1.77 – 6.66 12.25 0.31 0.25 – 3.99 – – – – 1.27 10 None 84 – – 0.90 – 4.90 – 5.02 – 0.38 – – 3.13 – – 3.4 1.22 Post- Nubian 84 None 90 – – – 0.16 6.79 14.89 5.32 – – – 1.77 – – 0.07 1.02 1.05 8 Rain 9 87.2 12.8 1.36 – 3.66 16.85 – – 0.39 – 1.84 3.39 – – – – 94 Rain 17 69.50 30.50 1.25 – – – – – 0.24 3.84 6.04 1.66 – 0.22 – – 95 Rain 18 21.40 78.60 – – 7.79 24.55 22.11 – 0.69 1.44 6.34 – – – – Quaternary aquifer 24 Rain 19 21.50 78.50 – – 5.06 18.49 13.79 – 0.39 – 5.56 0.93 – – – – (Upstream) 103 Rain 51 26.5 73.5 2.54 – 4.62 – – – 0.10 0.88 3.37 3.58 – – – – 103 Rain 53 65.9 34.1 0.51 – 2.68 – – – 0.19 – 1.28 2.20 – 0.22 – – 101 Rain 54 77 23 4.46 2.95 – – – – 0.72 – 5.19 – 4.48 0.65 – – Mixing Models 44 Nile 28 14.5 85.5 2.29 2.33 – – – 0.09 0.42 – 0.34 – – 0.28 – – Quaternary 44 Nile 32 39.7 60.3 1.15 1.22 – – – 0.17 1.08 1.55 – – 0.19 – – aquifer (Down- 44 Nile 36 41 59 0.22 3.45 – 9.66 – 6.48 – – 7.67 – – 3.36 – – stream) 44 Nile 45 52 48 – 1.25 – 9.55 – 0.22 – 4.86 – 5.11 2.78 – – 101 Rain 20 82 18 0.88 0.57 – – 2.02 – 0.02 – 0.66 – – 0.46 – – Post- 92 Rain 21 93.5 6.5 5.04 3.05 – – 8.24 – 0.47 – 3.19 – – 0.06 – – Nubian 101 Rain 22 87.8 12.2 1.5 1.26 – – – – 0.22 0.64 1.04 0.61 – – – – Note: Cal = calcite; Dol = dolomite; Gyp = gypsum; Hal = halite; Si = silica; Ilt = illite; Chrt = chlorite; Mont = Ca-montmorillonite; Albt = albite; An = anorthite, Alun = alunite; Ex = exchange; Ev = evaporation factor. Well locations for initial water-1, initial water-2, and final waters are indicated in Figures 1 and 10. Appl. Sci. 2022, 12, 8391 17 of 21 The water–rock interaction models well describe the evolution and salinization pro- cesses of the Quaternary groundwater located at the upstream watershed of Wadi Qena. Geochemical water–rock interaction modeling results suggest the dissolution of calcite, gypsum, halite, silica, illite, and chlorite as groundwater flows downward; dolomite, al- bite, anorthite, and alunite are precipitated, and some cation exchange occurs (e.g., from initial water-1 represented by sample 54 to final water at sites 55, 57, 58; from site 57 to 59; site 59 to 66, and site 66 to 71; see Table 4 and Figure 10). The evaporation factor for groundwater in this area ranges from 1.04 to 1.2. Groundwater in the PNA evolved from site 10 (initial water-1) to site 84 (final water), and then from site 84 (initial water-1) to site 90 (final water). The model converges via the dissolution of calcite, gypsum halite, and silica; de-dolomitization; precipitation of albite and anorthite; some cation exchange; and an evaporation factor ranging from 1.05 to 1.22. Figure 10. Schematic cross-section showing the geochemical processes controlling groundwater quality based on NETPATH geochemical model results reported in Table 4. To simulate the recharge and mixing from Nubian groundwater toward the other two aquifers, eleven model scenarios were converged for the Quaternary aquifer and three models for the Post-Nubian aquifer. To simulate upward leakage from the NSA toward the Quaternary groundwater aquifer located upstream, Nubian groundwater sites 8, 94, 95, 24, 103, and 101 were used as initial water-1, rainwater was used as initial water-2, and Quaternary groundwater sites 9, 17, 18, 19, 51, 53, and 54 were used as final waters in the NETPATH model. Model results for the shallow Quaternary groundwater aquifer located upstream of the Qena basin close to the confined NSA primarily indicated dissolution of calcite, gypsum, dolomite, halite, chlorite, and albite, and that clay minerals (illite, Ca-montmorillonite) and alunite were formed (Table 4). The estimated mixing percentages from the Nubian toward the Quaternary groundwater ranged from 21.4 % to 87.2 %; the recharge percentages from rainwater ranged from 78.6 % to 12.8%. The mixing NETPATH model results suggest that the downstream Quaternary alluvial groundwater aquifer located in the Wadi Qena delta area is mainly recharged from canal water (River Nile branches). The calculated mixing ratio ranged from 48% from original groundwater that comes from the upstream watershed represented by site 44 (final water at site 45) to 85.5% from Nile water (final water at site 28). The calculated mixing percentage from Appl. Sci. 2022, 12, 8391 18 of 21 Nubian to Post-Nubian groundwater ranged from 82 % to 93.5 % of Nubian groundwater, whereas the rainwater amount ranged from 6.5% to 18 %. Calculated mineral saturation indices (SI; Table 5) were consistent with changes in mineral phases, where the minerals that had negative saturation indices were dissolved and indicated by positive (+ve) mass transfer values in the NETPATH model, with the exception of de-dolomitization driving the dissolution of dolomite despite over-saturated SIs [60]. Table 5. Mineral saturation indices for phases in NETPATH geochemical models. Mineral Phases Well Aquifer No. Cal Dol Gyp Hal Si Ilt Chrt Mont Albt An Mic Alun 5 0.66 1.53 0.86 4.86 0.96 6.12 5.48 6.90 0.88 0.26 13.93 6.92 9 0.34 0.79 1.21 4.56 0.99 5.05 3.60 5.07 0.99 0.26 12.05 0.66 17 0.00 0.05 1.92 5.43 1.30 2.63 0.96 2.86 0.64 0.87 9.48 1.97 18 0.01 0.15 0.53 4.97 2.77 1.26 3.28 0.96 4.76 2.83 6.60 2.30 19 0.19 0.66 0.67 5.16 1.06 4.30 0.86 5.00 0.10 0.49 11.27 1.86 28 0.13 0.25 1.96 6.89 0.89 5.81 1.19 6.12 0.28 0.49 12.99 0.82 32 0.12 0.24 1.25 6.16 0.84 5.78 0.08 6.47 0.63 0.64 12.91 2.78 36 0.23 0.34 0.63 5.23 0.65 6.63 0.81 7.50 1.59 1.18 13.83 4.94 44 0.76 1.31 0.78 5.57 2.74 1.37 0.66 1.65 4.70 2.84 6.20 0.89 45 0.14 0.38 0.77 5.22 2.76 0.81 4.43 0.68 4.72 3.12 7.31 3.60 Quaternary 51 0.54 1.74 0.84 6.08 1.05 5.83 7.79 7.27 0.27 0.32 13.59 6.82 53 0.09 0.53 0.26 5.48 1.04 6.08 2.46 7.01 1.04 0.78 13.66 6.39 54 0.18 0.19 1.36 5.43 1.05 4.95 1.17 5.42 0.63 0.17 11.98 0.84 55 0.88 2.14 1.18 5.21 1.05 5.85 6.41 7.10 0.63 0.21 13.55 6.02 57 0.71 1.26 1.12 5.15 1.05 6.10 4.08 7.08 0.66 0.12 13.77 6.51 58 0.04 0.03 0.32 4.58 1.04 6.08 2.07 6.99 0.94 0.63 13.62 6.53 58 0.17 0.47 0.41 4.58 1.04 6.14 4.39 7.25 0.93 0.42 13.81 7.57 71 0.14 58.00 0.23 4.13 1.03 6.31 1.85 7.03 1.15 0.86 13.98 7.09 60 0.32 0.58 0.30 4.50 1.04 6.13 2.12 3.45 1.03 0.57 13.71 6.78 66 0.21 0.65 0.10 4.39 1.04 6.33 2.04 7.00 1.02 0.76 2.04 7.05 10 0.10 0.31 0.43 4.55 0.96 5.03 1.57 5.63 0.73 0.76 12.06 3.06 20 0.26 0.80 1.00 5.56 0.99 4.65 0.85 5.51 0.17 0.45 11.71 2.29 21 0.37 1.11 1.00 5.37 0.96 5.57 2.26 6.45 0.53 0.65 12.94 3.87 22 0.28 0.30 0.97 5.51 2.75 1.55 0.37 1.72 4.81 2.93 6.04 0.99 Post-Nubian 23 1.12 2.24 1.25 5.40 1.19 4.62 5.85 5.80 0.29 0.33 12.20 5.50 26 0.03 0.26 0.36 4.46 0.96 5.76 1.77 6.23 1.12 0.91 12.96 3.64 90 0.10 0.47 0.10 4.09 1.03 6.33 1.88 7.02 1.19 0.80 14.01 7.21 84 0.14 0.58 0.03 4.32 1.03 6.31 1.85 7.03 1.15 0.86 13.98 7.09 4 0.02 0.01 1.88 5.03 1.24 1.85 1.70 2.20 0.73 0.89 8.43 2.91 8 0.39 0.79 2.03 4.94 1.18 2.39 5.49 2.11 0.24 0.65 8.86 5.00 24 0.42 0.76 1.16 5.22 1.23 2.25 5.24 2.13 0.67 0.38 8.79 3.02 94 0.67 1.32 1.24 5.33 1.05 6.01 3.74 6.95 0.55 0.21 13.64 5.66 Nubian aquifer 95 0.56 1.13 1.36 5.28 1.05 5.89 3.85 6.95 0.59 0.22 13.46 5.24 92 0.57 1.17 1.17 5.21 1.05 6.02 3.61 6.95 0.61 0.28 13.66 5.68 101 0.54 1.33 0.83 5.37 1.05 6.07 4.02 6.97 0.53 0.41 13.78 6.20 103 1.31 3.00 2.63 5.16 1.05 5.84 8.93 6.85 0.67 0.43 13.79 4.34 Rain Rain 1.25 2.53 2.87 8.85 2.71 1.13 7.88 0.05 6.20 3.57 6.65 0.35 Nile Nile 0.15 0.37 2.25 8.07 2.74 1.35 3.30 1.34 5.78 3.42 6.44 1.52 Note: Cal = calcite; Dol = dolomite; Gyp = gypsum; Hal = halite; Si = silica; Ilt = illite; Chrt = chlorite; Mont = Ca-montmorillonite; Albt = albite; An = anorthite; Alun = alunite; Ex = exchange; and Ev = evapo- ration factor. Well locations for initial water-1, initial water-2, and final waters are indicated in Figures 1 and 10. Appl. Sci. 2022, 12, 8391 19 of 21 6. Conclusions The current study utilized hydrogeochemistry and environmentally stable isotopes to determine the main recharge sources and geochemical processes affecting groundwater in the Qena basin, located in the Eastern desert of Egypt. This basin comprises three main groundwater aquifers: the Quaternary aquifer, the Post Nubian aquifer (PNA), and the Nubian Sandstone aquifer (NSA), which is mainly controlled by lithological and structural features. Groundwaters in the upstream watershed generally had fresh to brackish water, 18 2 whereas those downstream were mainly brackish to saline. Isotopic data ( O and H) revealed that Nubian groundwater was relatively depleted, primarily of meteoric origin and a paleo-water recharged in a cooler climate. The NSA had higher groundwater temperatures than the other aquifers. Quaternary groundwater located at the upstream watershed received considerable recharge from recent meteoric water and upward leakage from the NSA. The downstream Quaternary aquifer in the delta of the Qena basin was characterized by mixed groundwater composed of upstream water with recent River Nile water. Isotopic analysis confirmed recharge of the Post-Nubian groundwater aquifer mainly from upward leakage from the NSA under artesian conditions and seepage from the upper unconfined Quaternary aquifer. NETPATH geochemical model results indicated that the evaporation process, water–rock interaction, and mixing are the physical and geochemical processes controlling groundwater quality, where leaching and dissolution processes of terrestrial minerals and silicate weathering prevail. The Nubian groundwater aquifer has a great expanse, considerable thickness, possesses good groundwater quality, and should be well explored and well managed for sustainable groundwater use. Author Contributions: A.R.: Carried out the fieldwork and chemical analysis and field data interpre- tation for the geochemical groundwater characteristics. M.E.: Carried out the fieldwork, conceived of the presented idea, and write the part of the methodology, as well as interpretation of geochemi- cal and isotopic data and contribute in writing the whole manuscript with input from all authors. I.E.S.: revise the whole manuscript and propose the research point, E.D.: Carried out measurements for stable environmental isotopes at her laboratory. M.S.: Carried out the interpretation of geo- chemical analyses for surface and groundwater samples. and S.M.: Shared with writing the part on groundwater geochemistry, in addition, she wrote part of the result and discussion in the manuscript. All authors have read and agreed to the published version of the manuscript. Funding: This research received no external funding. Institutional Review Board Statement: Not applicable. 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