AbstractThis study aimed to explore the relative importance of mesohabitat and microhabitat features, as well as the spatial and within‐day temporal covariates, on the body size‐related within‐reach spatial distribution of stream‐dwelling fishes in a highland‐type and a sub‐mountainous‐type stream in Central Europe. During daytime, point abundance sampling was applied to catch the fish, and environmental data were recorded at the sampling points (microhabitat features) and along the transects that crossed the sampling points (mesohabitat features). Variance partitioning revealed similar patterns in the size‐classified fish data for the two streams. Microhabitat features had a greater explained variance than mesohabitat features. The majority of the mesohabitat influence emerged as variance shared with the microhabitat influence. The pure spatially explained variance proportion was lower than the variance explained purely by the environmental features (meso and micro together), and no temporally explained variance was found. Many species showed body size‐related environmental associations. The results suggest that the different‐scale habitat features act in a hierarchical way on the within‐reach fish distribution. Meso‐scale features may determine a great proportion of the micro‐scale habitat variability and micro‐scale conditions may directly affect how fish select places to stay as a function of both species identity and body size. The restoration of meso‐scale environmental diversity can effectively contribute to the protection of size‐structured populations in sub‐mountainous and highland streams.