Managed aquifer recharge (MAR), a hydro-geological intervention designed to dilute groundwater salinity, pumps pond water treated through a slow sand filter into the underground aquifers. We evaluated the microbiological safety of the resulting MAR water at sites from three districts in southwest coastal Bangladesh. We collected monthly paired pond-MAR water samples from July 2016-June 2017 and enumerated fecal coliforms and E. coli using the IDEXX quanti-tray technique, by the most probable number (MPN) method. We used WHO risk categories for microbiological quality; no risk (<1 MPN), low risk (1-10 MPN) and moderate to high risk (>10 MPN per 100 mL water). We estimated the difference in mean log10 MPN in pond and MAR water using linear mixed effect models with random intercepts and cluster adjusted robust standard error. Almost all pond water samples (292/299, 98%) had moderate-to high-risk level (>10 MPN) fecal coliforms and E. coli (283/299, 95%). In contrast, 81% (242/300) of MAR water samples had no or low risk level fecal coliforms (0-10 MPN), of which 60% (179/300) had no fecal coliforms. We detected no or low risk level E. coli in 94% (283/300) of MAR water samples of these 80% (240/300) had no E. coli. MAR samples had lower mean log10 MPN fecal coliforms (-2.37; 95% CI: -2.56, -2.19) and E. coli (-2.26; 95% CI: -2.43, -2.09) than pond water; microbial reductions remained consistent during the wet (May-October) and dry seasons. MAR-systems provided water with reduced fecal indicator bacteria compared to infiltered pond water.