This study examined the relative importance of climate change and drinking-water treatment for gastrointestinal illness incidence in children (age <5 years) from period 2046–2065 compared to 1991–2010. The northern Wisconsin (USA) study focused on municipalities distributing untreated groundwater. A time-series analysis first quantified the observed (1991–2010) precipitation and gastrointestinal illness associations after controlling for seasonality and temporal trends. Precipitation likely transported pathogens into drinking-water sources or into leaking water-distribution networks. Building on observed relationships, the second analysis projected how climate change and drinking-water treatment installation may alter gastrointestinal illness incidence. Future precipitation values were modeled by 13 global climate models and three greenhouse-gas emissions levels. The second analysis was rerun using three pathways: (1) only climate change, (2) climate change and the same slow pace of treatment installation observed over 1991–2010, and (3) climate change and the rapid rate of installation observed over 2011–2016. The results illustrate the risks that climate change presents to small rural groundwater municipalities without drinking water treatment. Climate-change-related seasonal precipitation changes will marginally increase the gastrointestinal illness incidence rate (mean: ∼1.5%, range: −3.6–4.3%). A slow pace of treatment installation somewhat decreased precipitation-associated gastrointestinal illness incidence (mean: ∼3.0%, range: 0.2–7.8%) in spite of climate change. The rapid treatment installation rate largely decreases the gastrointestinal illness incidence (mean: ∼82.0%, range: 82.0–83.0%).