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The recharge flow paths in a typical weathered hard-rock aquifer in a semi-arid area of southern India were investigated in relation to structures associated with a managed aquifer recharge (MAR) scheme. Despite the large number of MAR structures, the mechanisms of recharge in their vicinity are still unclear. The study uses a percolation tank as a tool to identify the input signal of the recharge and uses multiple measurements (piezometric time series, electrical conductivity profiles in boreholes) compared against heat-pulse flowmeter measurements and geochemical data (major ions and stable isotopes) to examine recharge flow paths. The recharge process is a combination of diffuse piston flow and preferential flow paths. Direct vertical percolation appears to be very limited, in contradiction to the conceptual model generally admitted where vertical flow through saprolite is considered as the main recharge process. The horizontal component of the flow leads to a strong geochemical stratification of the water column. The complex recharge pattern, presented in a conceptual model, leads to varied impacts on groundwater quality and availability in both time and space, inducing strong implications for water management, water quality evolution, MAR monitoring and longer-term socio-economic costs.