Reservoir sedimentation and water quality degradation remain critical threats to water supply and dam safety in tropical semi-arid regions. This study presents an integrated assessment of hydrological variability, water quality, and sediment contamination at Kiri Dam, Nigeria. Using a 43-year dataset (1982–2024), rainfall and discharge trends were evaluated with the Mann–Kendall test and Sen’s slope estimator, while seasonal field sampling in 2024 covered physicochemical, nutrient, microbial, and heavy metal parameters across seven reservoir sites. Risk indices, including the Water Quality Index (WQI), Pollution Load Index (PLI), geo-accumulation index (I_geo), enrichment factor (EF), and irrigation suitability metrics, were applied, supported by principal component analysis (PCA) and regression modelling. Results indicated no significant rainfall trend (Z = +1.24, p = 0.217; Sen’s slope = +1.3 mm yr⁻¹) but a significant increase in discharge (+1,353 m³ s⁻¹ yr⁻¹, p < 0.01). Wet-season turbidity exceeded WHO/NSDWQ limits by >100-fold (556–573 NTU), coinciding with cadmium (0.018 mg L⁻¹) and lead (0.11 mg L⁻¹) surpassing permissible values (0.003 and 0.01 mg L⁻¹, respectively). Microbial counts exceeded 200 CFU/100 mL at inflow and reservoir-bed zones, confirming faecal contamination. Sediment analysis revealed cadmium enrichment (7–10 mg kg⁻¹), PLI > 1.5, and EF > 10 at inflow and bed sites, classifying them as heavily polluted. PCA grouped turbidity, TSS, Cd, and Pb as codrivers, while regression confirmed turbidity and Cd as strong predictors of WQI (adjusted R² = 0.72). Overall, reservoir risks are driven more by sediment–water interactions and operational discharges than by rainfall variability, highlighting the urgent need for adaptive management, including sediment dredging, erosion control, and advanced treatment to safeguard water supply, irrigation, and ecological health.