Chiatura Municipality, located in the Imereti region of Georgia, represents one of the country's most environmentally vulnerable mining areas due to more than a century of intensive manganese extraction and ore-processing activities. This study evaluates the contamination risks associated with manganese and selected heavy metals (Cu, Zn, Pb, Cd, Ni, and Co) in the Kvirila River and adjacent spring waters during the period 2024–2026. Water, suspended solids, and bottom sediment samples were collected from both background and mining-affected locations and analyzed using modern analytical methods that comply with European environmental monitoring standards. The concentrations of total manganese and heavy metals were determined, and contamination levels were assessed through comparison with maximum permissible concentrations and hazard quotient (HQ) indices. The results indicate that manganese is the principal contaminant affecting the aquatic environment. Although the concentrations of Cu, Zn, Pb, Cd, Ni, and Co remained below their respective regulatory limits, manganese concentrations in the Kvirila River exceeded acceptable risk thresholds (HQsw > 1), indicating potential environmental and ecological risks. In contrast, manganese levels in spring waters remained below the hazard threshold (HQdw < 1), suggesting no significant health risk for groundwater resources. Elevated manganese concentrations were also detected in river suspended solids and bottom sediments, confirming long-term accumulation associated with mining activities. The findings provide valuable scientific evidence for environmental monitoring and sustainable water resource management in mining-affected regions.