Comprehensive Everglades Restoration Plan (CERP) objectives include the return of more natural salinity regimes to the bays and estuaries of southern Florida (U.S.A.). We examined for spatiotemporal patterns in rainwater killifish (Lucania parva) density and size with emphasis on relations with salinity, salinity variation, submerged aquatic vegetation (SAV), temperature, and depth. Using linear quantile mixed models (LQMM) and cluster analyses, we analyzed 18 consecutive wet-dry seasons (9 years) of enclosure trap data from 44 fixed stations along mainland shoreline of southern Biscayne Bay, Florida. The LQMM results suggested that SAV was the strongest influencing, and (potentially) most limiting, habitat variable on killifish density, and that decreases in mean salinity and salinity variation may result in higher killifish densities in our study domain. Killifish sizehabitat relationships were few. Cluster analysis of stations, based on killifish densities across time, failed to reveal clear spatial fish density gradients, consistent density hot-spots, or grouping according to median habitat conditions. However, cluster analysis of seasons, based on killifish densities across space, indicated that high densities were associated with the wet season and low densities with the dry, although this depended on year. Our analyses suggest that realization of lower salinities and lower salinity variation in our study domain, if they are not accompanied by SAV decreases, may enhance killifish populations and/or their role as prey. Owing to its high stress-tolerance and extreme variability in density, L. parva is not an ideal indicator species of CERP-modified salinity conditions, but warrants tracking as restoration activities ensue.