The role abiotic factors play in structuring communities is one of the fundamental questions in ecology. At small spatial and temporal scales, abiotic conditions influence patterns of species movement and habitat use. At larger scales, abiotic factors affect patterns of species abundance and distribution. The structuring effect of abiotic conditions may be particularly important along ecotonal habitats. In the southwestern Everglades, mangrove-lined creeks link freshwater marshes to estuarine habitats. This study examined the spatial and temporal dynamics of fish communities along oligohaline to mesohaline reaches of tidal creeks within the southwest region of Everglades National Park. Ten sites in the upper Shark River Estuary were sampled during the wet, early-dry, and mid-dry seasons of 2004-2008, utilizing electrofishing and trapping methods. Abundance and species composition differed across seasons and years. Overall, fish and macroinvertebrate catches were higher and more diverse in the upper most sites, particularly during the drier sampling periods. This pattern reflects an influx of freshwater taxa, both small-bodied prey and larger-bodied fish predators, into mangrove creeks at the ecotone as water levels upstream recede and marshes dry. Influxes of freshwater species were short-lived, particularly for smaller taxa, suggesting heavy predation once small taxa move from upstream shallow marshes into tidal creeks. Inclusion of marsh water levels increase model fit for a subset of analyses. At the same time, the incidence and abundance of certain predatory marine transient and estuarine resident fishes increase at these sites resulting in high predator-prey co-occurrence at the ecotone during the dry season. Fish catches were positively related to oxygen levels, and negatively related to salinity. In contrast, variation in palaemonid shrimp species across the estuary were not explained by salinity nor oxygen. Instead, stable isotope signatures suggest segregation of energy sources along the estuary in the dry season, but some dietary convergence in the wet season, due perhaps to animals moving and foraging with tides. Our results indicate that ecotonal creeks may serve as important dry-season refugia for freshwater taxa, and that pulses of freshwater taxa into tidal creeks may also increase seasonal foraging opportunities for transient oligohaline and mesohaline species. Restoration and recovery of historic freshwater inflow within the Everglades ecosystem may reverse this trend, prolonging the pooling of freshwater in upland marshes.