Flooding is the most frequent natural hazard globally, but evidence of its impact on domestic water point contamination remains limited. This study aimed to assess dam-related flooding's impact on microbiological contamination of rural water points and to evaluate agreement of satellite-derived flood maps with ground-based observations of water point flooding. Fieldwork took place in two Ghanaian districts frequently flooded following dam overspill. Fifty-seven water points were tested for bacterial parameters during and immediately after flooding. Forty water points were resampled in the dry season, with the remainder having run dry. Ground-based observations of flooding were compared with three satellite-derived flood maps. Boreholes were less contaminated than wells or surface waters (geometric mean E. coli = 20.2, 175.6, and 590.7 cfu/100 ml, respectively). Among groundwater points, a Wilcoxon signed-rank test indicated significantly greater median E. coli and thermotolerant coliform contamination during flooding (p = 0.025 and p < 0.001, respectively), but Shigella, salmonella, and intestinal enterococci counts were not significantly different between seasons. In contrast, among surface water points, E. coli, Shigella, and Salmonella counts were significantly greater in dry season samples (p < 0.005 for all parameters), possibly reflecting a "concentration" effect. Satellite-derived flood maps had no or low agreement with ground-based observations of water point flooding. Although groundwater quality deteriorated during and after flooding, surface waters were the most microbiologically contaminated in both seasons. The greatest public health risk thus occurred where households switched to surface water collection during or following flood season. Flood risk should be assessed before borehole installation and existing flood-prone boreholes remediated to mitigate population exposure to contaminated water.