Continuous monitoring, analysis, and mapping of groundwater depth (GD) and electrical conductivity (EC) are critical for sustainable water management in irrigated agricultural regions. This study evaluates spatiotemporal variations in GD and EC within the Aksu Irrigation System (Türkiye) over 2005–2024 using Mann–Kendall trend analysis and geographic information systems (GIS)-based geostatistical methods. The results indicate that groundwater depth (GD) trends are generally relatively favorable across the study area, despite relatively unfavorable initial conditions. In contrast, increasing EC trends were identified in 38% of the study area, mainly concentrated in the central and northern zones, whereas the remaining areas exhibited relatively favorable conditions. In terms of baseline salinity conditions, no areas exceeded the critical threshold for EC initial values, indicating acceptable groundwater salinity levels at the beginning of the study period. Groundwater-related risk was assessed based on combined GD and EC characteristics influencing root zone conditions, including waterlogging potential and salinity development. The integrated risk map, based on the 2005–2024 assessment period, indicates that 25% of the study area is relatively unfavorable, while 75% is relatively favorable. The proposed approach provides a practical and spatially explicit tool for groundwater risk evaluation, supporting improved water management in large-scale irrigation systems.