We determined how environmental variability affected distributions of seasonally recruiting fishes (i.e., transient species) in coastal lagoons of Maryland from May–October during 1996, 1997, and 1999. A total of 241 monthly sampling events were conducted in the coastal lagoons at 40 sampling stations. Fluctuations in salinity resulting from variation in stream discharge were negatively correlated with intra-annual stability of fish assemblages. Transient, or non-resident species (e.g., recruiting species), were more frequent in habitats where salinity was less variable. When stream discharge lessened during dry years, transient species were more common throughout the coastal lagoons. Thus, environmental variability influenced distributions of young-of-year fishes in coastal estuaries.