Water resources in Makindu Sub-County, Makueni County, Kenya, are under severe stress from converging environmental and anthropogenic factors. This study employed GIS-based remote sensing, meteorological time-series analysis, participatory GIS (PGIS) mapping, and quantitative regression modelling to assess the combined effects of rainfall variability, temperature change, and land use/land cover change (LULCC) on major water resources across the period 1994–2024. SPOT satellite imagery classified across four epochs (1994, 2004, 2014, 2024) using Maximum Likelihood Classification documented substantial LULCC, while Kenya Meteorological Department records and CHIRPS gridded data were analysed for hydro-climatic trends. A PGIS inventory covering nine sub-locations quantified functional boreholes, seasonal rivers, dams, water pans, and springs for each epoch. Simple linear regression, multiple regression, and chi-square analyses were conducted in SPSS Version 25. Results reveal a 2,400% increase in functional boreholes (3 to 75) driven by population growth and surface water depletion, while seasonal rivers remained stable but showed critical sub-location-level deterioration, dams and water pans increased from 25 to 37 through community investment, and springs remained constant at 4 functional units across all four epochs. Rising mean annual temperatures (R² = 0.958–0.982; p < 0.01) and declining rainfall were statistically associated with surface water loss across seasonal rivers, dams, and water pans, while springs remained stable at 4 functional units unresponsive to temperature, rainfall, or population change reflecting deep aquifer supply. The study provides a comprehensive evidence base for multi-stakeholder water resource management and policy development in semi-arid Kenya.