In the current study, subsurface characteristics within the complex formation of the Shilabati basin system of West Bengal, India, extending over an area of 3888 km2, have been estimated using a cost-effective piezometer and MIKE FEFLOW package based on a steady-state numerical model. Pore size and fine particle content of streambeds are affected by two opposing flow contraptions. Such opposite flow conditions are likely to affect the hydraulic conductivity of the streambed. However, analogies of the hydraulic conductivity (Kh) of streambeds for losing and gaining streams have not been well documented in the recent past. The Kh value from the piezometer has been highest at the Dakshin Pairachali site (6.765 m/day), with the stream gaining water from the discharge of the local aquifer. Analysis of the stream-aquifer interaction using the FEFLOW model has allowed us to understand the groundwater water head of the basin ranging from 160.33 to 0.32 m.a.s.l (meters above sea level). The present study also constitutes the first attempt for the identification of suitable sites for the implementation of managed aquifer recharge (MAR) technology in West Bengal, India, to manage extreme drought events. The suitable sites have been identified by means of three fuzzy multi-criteria decision analysis based on nine criteria: river discharge, moisture content, porosity, drainage type, rainfall, land use type, geology, aquifer material, and hydraulic conductivity. To design a radial collector well and infiltration gallery for the selected site in an anisotropic, homogeneous, unconfined, and semi-infinite aquifer near a fully penetrating stream, a pumping test has been conducted to optimize a safe yield of 12.096 MLD (megaliters per day).