Animal populations are typically structured by space and body size. Quantifying these dynamics is critical to not only understanding their spatial population ecology but also informing their conservation and management. Here, I present some recent studies using individual mark-recapture data (e.g., PIT tags) to elucidate the spatial population dynamics of stream fishes. In one study from the southeastern USA, I will present how stream fish movement (immigration and emigration) differed over space, time, and body size class. This study demonstrates an approach of combining mark-recapture data and count data to gain deeper demographic information using an integrated population model. In a second study conducted in Japan, size-structured meta-population dynamics were quantified for native stream salmonids using 9-year mark-recapture data and this information was used to evaluate the temporal stability of meta-population dynamics depending on different degrees of spatial population synchrony. Overall, mark-recapture studies of stream fish, albeit labor-intensive, provide rich information on individual variation and its consequences on higher-order patterns (i.e., population dynamics), which would not have been obtained based on analysis of unmarked data.