Many water-related illnesses show an increase during the wet season. This is often due to fecal contamination from runoff, yet, it is unknown whether seasonal changes in water availability may also play a role in increased illness via changes in the type of primary water source used by households. Very little is known about the dynamic aspects of access to water and changes in source type across seasons, particularly in semi-arid regions with annual water scarcity. The research questions in this study were: (1) To what degree do households in Uganda (UG) and Tanzania (TZ) change primary water source type between wet and dry seasons?; and (2) How might seasonal changes relate to water quality and health? Using spatial survey data from 92 households each in UG and TZ this study found that, from wet to dry season, 26% (UG) and 9% (TZ) of households switched from a source with higher risk of contamination to a source with lower risk. By comparison, only 20% (UG) and 0% (TZ) of households switched from a source with lower risk of contamination to a source with higher risk of contamination. This research suggests that one pathway through which water-related disease prevalence may differ across seasons is the use of water sources with higher risk contamination, and that households with access to sources with lower risks of contamination sometimes choose to use more contaminated sources.