Drinking water related infections are expected to increase in the future due to climate change. Understanding the current links between these infections and environmental factors is vital to understand and reduce the future burden of illness. We investigated the relationship between weekly reported cryptosporidiosis and giardiasis (n = 7,422), extreme precipitation (>90th percentile), drinking water turbidity, and preceding dry periods in a drinking water system located in greater Vancouver, British Columbia, Canada (1997–2009) using distributed lag non-linear Poisson regression models adjusted for seasonality, secular trend, and the effect of holidays on reporting. We found a significant increase in cryptosporidiosis and giardiasis 4–6 weeks after extreme precipitation. The effect was greater following a dry period. Similarly, extreme precipitation led to significantly increased turbidity only after prolonged dry periods. Our results suggest that the risk of cryptosporidiosis and giardiasis increases with extreme precipitation, and that the effects are more pronounced after a prolonged dry period. Given that extreme precipitation events are expected to increase with climate change, it is important to further understand the risks from these events, develop planning tools, and build resilience to these future risks.