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This comprehensive dataset describe the groundwater quality and microbial risk assessment from shallow drinking water sources across seven flood-affected districts of Sindh Province, Pakistan following the 2022 monsoon floods. The dataset includes measurements of key physicochemical parameters and microbiological indicators obtained from 1,795 groundwater samples collected from commonly used rural drinking water sources such as hand pumps, motor pumps, and tube wells. In addition to measured water quality parameters, the dataset includes derived indicators such as the Water Quality Index (WQI) and Quantitative Microbial Risk Assessment (QMRA) outputs based on the Beta–Poisson dose–response model. The dataset also provides spatial summaries, district-level exceedance of drinking water standards, and infection and illness probability estimates across different demographic groups. These data provide an important baseline resource for understanding post-flood groundwater conditions and may support future research on groundwater monitoring, microbial risk assessment, and water safety management in flood-prone regions.