Waterlogging, soil salinization, and groundwater depletion in non-rechargeable aquifers are among the causes endangering the sustainability of Siwa Oasis. The water resources include the tertiary carbonate aquifer (TCA), Nubian sandstone aquifer (NSSA), springs, drains, and hypersaline lakes. Geophysical logs were used to identify various aquifer systems. Stable isotopes, major ions, and heavy metals were examined. K-means cluster analysis based on principal component analysis (PCA), hydrochemistry, stable isotopes, and mixing models using NETPATH were applied in order to understand the complex hydrogeological conditions in the different aquifer systems. The results showed that all water samples were under-saturated (SI < 1) with respect to anhydrite, halite, and gypsum minerals, indicating the water's ability to dissolve more from these minerals and increase water salinity.In contrast, calcite, dolomite, Ca-montmorillonite, and illite minerals were supersaturated in most water samples (SI > 1), showing their ability to precipitate these minerals. There is no recharge for the aquifer systems, and all the groundwater resources have paleo meteoric origin, where the maximum values of δ18O and δ2H are −8.45 and −65.63, respectively. All of the springs originated from the TCA, as indicated from the K-mean cluster analysis. There is a rapid increase in the water salinity of the TCA from 1998 to 2022 due to evaporation, rock weathering, mixing with old trapped sea water, and seepage of saline water from salt lakes. The significant variations in the water salinity of the TCA aquifer are due to the mixing between fresh water of NSSA (dilution) and salt water from Zeituna and Siwa lakes through downward flow in some locations, where over-extraction of water for irrigation purposes has decreased the water pressure in the TCA. The mixing model confirmed salt lakes' contribution in increasing the TCA salinity by 2%–4%. Mixing water from TCA and NSSA could be the best management of the water resources in Siwa Oasis, as well as the application of subsurface drip irrigation. Display omitted •Approach integrates stable isotopes, PCA, K-Means cluster analysis with geochemical and mixing modelling.•Successful characterization of TCA, NSSA, drains, springs and lakes recharge sources and controlling factors.•Mixing, evaporation, water-rock interaction, control surface water and groundwater chemistry.•Water resources management through application of subsurface drip irrigation, mixing water of TCA and NSSA, and artificial lake.