Climate change is expected to affect air temperature and watershed hydrology, but the degree to which these concurrent changes affect stream temperature is not well documented in the tropics. How stream temperature varies over time under changing hydrologic conditions is difficult to isolate from seasonal changes in air temperature. Groundwater and bank storage contributions to stream flow (i.e., base flow [BF]) buffer water temperatures against seasonal and daily fluctuations in solar radiation and air temperature, whereas rainfall-driven runoff produces flooding events that also influence stream temperature. We used a space-for-time substitution to examine how shifts in BF and runoff alter thermal regimes in streams by analyzing hydrological and temperature data collected from similar elevations (400–510 m above sea level) across a 3,500-mm mean annual rainfall gradient on Hawai'i Island. Sub-daily water temperature and stream flow gathered for 3 years were analyzed for daily, monthly, and seasonal trends and compared with air temperature measured at multiple elevations. Results indicate that decreases in median BF increased mean, maximum, and minimum water temperatures as well as daily temperature range. Monthly and daily trends in stream temperature among watersheds were more pronounced than air temperature, driven by differences in groundwater inputs and runoff. Stream temperature was strongly negatively correlated to BF during the dry season but not during the wet season due to frequent wet season runoff events contributing to total flow. In addition to projected increases in global air temperature, climate driven shifts in rainfall and runoff are likely to affect stream flow and groundwater recharge, with concurrent influences on BF resulting in shifts in water temperature that are likely to affect aquatic ecosystems.