Irrigation has made a significant contribution to supporting the population’s expanding food demands, as well as promoting economic growth in irrigated regions. The current investigation was carried out in order to estimate the quality of the groundwater for agricultural viability in the Algerian Desert using various water quality indices and geographic information systems (GIS). In addition, support vector machine regression (SVMR) was applied to forecast eight irrigation water quality indices (IWQIs), such as the irrigation water quality index (IWQI), sodium adsorption ratio (SAR), sodium percentage (Na%), soluble sodium percentage (SSP), potential salinity (PS), Kelly index (KI), permeability index (PI), potential salinity (PS), permeability index (PI), and residual sodium carbonate (RSC). Several physicochemical variables, such as temperature (T°), hydrogen ion concentration (pH), total dissolved solids (TDS), electrical conductivity (EC), K+, Na2+, Mg2+, Ca2+, Cl−, SO42−, HCO3−, CO32−, and NO3−, were measured from 45 deep groundwater wells. The hydrochemical facies of the groundwater resources were Ca–Mg–Cl/SO4 and Na–Cl−, which revealed evaporation, reverse ion exchange, and rock–water interaction processes. The IWQI, Na%, SAR, SSP, KI, PS, PI, and RSC showed mean values of 50.78, 43.07, 4.85, 41.78, 0.74, 29.60, 45.65, and −20.44, respectively. For instance, the IWQI for the obtained results indicated that the groundwater samples were categorized into high restriction to moderate restriction for irrigation purposes, which can only be used for plants that are highly salt tolerant. The SVMR model produced robust estimates for eight IWQIs in calibration (Cal.), with R2 values varying between 0.90 and 0.97. Furthermore, in validation (Val.), R2 values between 0.88 and 0.95 were achieved using the SVMR model, which produced reliable estimates for eight IWQIs. These findings support the feasibility of using IWQIs and SVMR models for the evaluation and management of the groundwater of complex terminal aquifers for irrigation. Finally, the combination of IWQIs, SVMR, and GIS was effective and an applicable technique for interpreting and forecasting the irrigation water quality used in both arid and semi-arid regions.