Anthropogenic climate change will likely increase diarrhea rates for communities with inadequate water, sanitation, or hygiene facilities including those with intermittent water supplies. Current approaches to study these impacts typically focus on the effect of temperature on all-cause diarrhea while excluding precipitation and diarrhea etiology while not providing actionable adaptation strategies. We develop a partially mechanistic, systems approach to estimate future diarrhea prevalence and design adaptation strategies. The model incorporates downscaled global climate models, water quality data, quantitative microbial risk assessment, and pathogen prevalence in an agent-based modeling framework incorporating precipitation and diarrhea etiology. It is informed using water quality and diarrhea data from Hubli-Dharwad, India-a city with an intermittent piped water supply exhibiting seasonal water quality variability vulnerable to climate change. We predict all-cause diarrhea prevalence to increase by 4.9% (Range: 1.5-9.0%) by 2011-2030, 11.9% (Range: 7.1-18.2%) by 2046-2065, and 18.2% (Range: 9.1-26.2%) by 2080-2099. Rainfall is an important modifying factor. Rotavirus prevalence is estimated to decline by 10.5% with Cryptosporidium and E. coli prevalence increasing by 9.9% and 6.3%, respectively, by 2080-2099 in this setting. These results suggest that ceramic water filters would be recommended as a climate adaptation strategy over chlorination. This work highlights the vulnerability of intermittent water supplies to climate change and the urgent need for improvements.