The current study integrates remote sensing, machine learning, and physicochemical parameters to detect hydrodynamic conditions and groundwater quality deterioration in non-rechargeable aquifer systems. Fifty-two water samples were collected from all water resources in Siwa Oasis and analyzed for physical (pH, T°C, EC, and TDS) chemical (SO42−, HCO3−, NO3−, Cl−, CO32−, SiO2, Mg2+, Na+, Ca2+, and K+), and trace metals (AL, Fe, Sr, Ba, B, and Mn). A digital elevation model supported by machine learning was used to predict the change in the land cover (surface lake area, soil salinity, and water logging) and its effect on water quality deterioration. The groundwater circulation and interaction between the deep aquifer (NSSA) and shallow aquifer (TCA) were detected from the pressure-depth profile of 27 production wells penetrating NSSA. The chemical facies evolution in the aquifer systems were (Ca–Mg–HCO3) in the first stage (freshwater of NSSA) and changed to (Na–Cl) type in the last stage (brackish water of TCA and springs). Support vector machine successfully predicted the rapid increase of the hypersaline lake area from 22.6 km2 to 60.6 km2 within 30 years, which deteriorated a large part of the cultivated land, reflecting the environmental risk of over-extraction of water for irrigation of agricultural land by flooding technique and lack of suitable drainage network. The waterlogging in the study was due to a reduction in the infiltration rate (low permeability) of the soil and quaternary aquifer. The cause of this issue could be a complete saturation of agricultural water with chrysotile, calcite, talc, dolomite, gibbsite, chlorite, Ca-montmorillonite, illite, hematite, kaolinite and K-mica (saturation index >1), giving the chance of these minerals to precipitate in the pore spaces of the soil and decrease the infiltration rate. The NSSA is appropriate for irrigation, whereas TCA is inappropriate due to potential salinity and magnesium risks. The best way to manage water resources in Siwa Oasis could be to use underground drip irrigation and combine water with TCA and NSSA. •Application of remote sensing, SVM, pressure-depth profile, PHREEQC, geochemical modeling, and IWQIs.•Increasing soil salinization, water logging, and surface area of lakes from 1990 to 2020.•Decline in the water pressure of the NSSA in the central part of Siwa Oasis.•Rapid water quality deterioration of the TCA from 1998 to 2022.•Water management using subsurface drip irrigation and mixing water of TCA and NSSA.