Climate change may impact human health through the influence of weather on environmental transmission of diarrhea. Previous studies have found that high temperatures and heavy precipitation are associated with increased diarrhea prevalence, but the underlying causal mechanisms are not clear. We linked measurements of Escherichia coli in source water (n=1,673), stored drinking water (n=8,924), and hand rinses from children <2 years old (n=2,660) with publicly available gridded temperature and precipitation data (at ≤0.2 degree spatial resolution and daily temporal resolution) by the GPS coordinates and date of sample collection. Measurements were collected over a 3-year period across a 2500 km2 area in rural Kenya. In drinking water sources, high 7-day temperature was associated with a 0.16 increase in log10 E. coli levels (p<0.001), while heavy 7-day total precipitation was associated with a 0.29 increase in log10 E. coli levels (p<0.001). In household stored drinking water, heavy 7-day precipitation was associated with a 0.079 increase in log10 E. coli levels (p=0.042). On child hands, high 7-day temperature was associated with a 0.39 decrease in log10 E. coli levels (p<0.001). Our findings provide insight on how climate change could impact environmental transmission of bacterial pathogens in Kenya, and suggest water treatment could be a mitigation strategy.