Adequate management and conservation of instream thermal habitats requires an understanding of the control that different landscape features exert on water temperatures. Previous studies have extensively explored the influence of spatial scale on these relationships. However, the effect of temporal scale remains poorly understood. Here, we use paired air–water mean daily and monthly summer temperatures collected over four years from 130 monitoring stations in Japanese mid‑ to low‑order streams to investigate whether perceived effects of different environmental controls on water temperature are dependent on the timescale of the temperature data, and whether those dependencies are related to the spatial scale at which these controls operate. We found a clear pattern for the significant cooling effect, high relative importance and strong dominance exerted by the riparian forest cover on daily temperatures at the reach scale becoming dampened by concomitant increases associated to the proportion of volcanic geology on monthly temperatures at the catchment scale. These results highlight the importance of contextualizing the effects of environmental controls on water temperatures to the timescale of the analysis. Such dependencies are particularly important for the management and conservation of instream thermal habitats in a rapidly warming world.