Climate change is expected to cause changes in precipitation quantity, intensity, frequency and duration, which will subsequently alter environmental conditions and might increase the risk of waterborne disease. The objective of this study was to describe the seasonality of and explore associations between weather, water quality and occurrence of infectious gastrointestinal illnesses (IGI) in two communities in Nunatsiavut, Canada. Weather data were obtained from meteorological stations in Nain (2005-2008) and Rigolet (2008). Free-chlorine residual levels in drinking water were extracted from municipal records (2005-2008). Raw surface water was tested weekly for total coliform and E. coli counts. Daily counts of IGI-related clinic visits were obtained from health clinic registries (2005-2008). Analysis of weather and health variables included seasonal-trend decomposition procedures based on Loess. Multivariable zero-inflated Poisson regression was used to examine potential associations between weather events (considering 0-4 week lag periods) and IGI-related clinic visits. In Nain, water volume input (rainfall + snowmelt) peaked in spring and summer and was positively associated with levels of raw water bacteriological variables. The number of IGI-related clinic visits peaked in the summer and fall months. Significant positive associations were observed between high levels of water volume input 2 and 4 weeks prior, and IGI-related clinic visits (P < 0.05). This study is the first to systematically gather, analyse and compare baseline data on weather, water quality and health in Nunatsiavut, and illustrates the need for high quality temporal baseline information to allow for detection of future impacts of climate change on regional Inuit human and environmental health.