The life histories of estuarine species are often adapted to the environmental variability they experience. However, estuaries are increasingly vulnerable to natural and anthropogenic changes, necessitating an understanding of how shifting conditions affect the survival, behaviour and population structure of estuarine-dependent animals. In this study we used data from fisheries-independent surveys collected across six estuaries with variable salinity regimes in Texas, USA, from 1975 to 2016 to investigate the role sources of freshwater inflow play in shaping juvenile bull shark Carcharhinus leucas size structure. High frequencies of co-occurrence with similarly sized conspecifics (59% of capture events) suggest bull sharks segregated within Texan estuaries based on body size. Bull shark sizes increased with distance to the nearest source of freshwater inflow, although effect sizes were small and access to freshwater habitats may be more important in shaping size-dependent distribution patterns. River mouths were disproportionately used by smaller juveniles (>90-cm total length, TL) and avoided by larger juveniles (<135cm TL). However, the use of river mouths decreased in estuaries characterised by limited freshwater inflow and greater variability in salinities at river mouths, highlighting geographic differences in the functions these habitats provide as potential environmental and predator refugia. Young-of-the-year (i.e. age-0) sharks also increased their use of river mouths throughout the 40-year study period, revealing the growing importance of river mouths as potential nursery habitats.