The pre-drainage Everglades (FL, USA) was a shallow slowly-flowing mosaic of wetland habitats (~10,000 km2). Due in part to drainage and compartmentalization in the 20th century, the spatial patterning of the ridge and slough landscape has been degraded by more than 25%. In some places, high densities of large sedges (sawgrass, Cladium jamaicense) have filled the historically deeper waterlily and spike-rush sloughs and the microtopographic relief has been lost. The impact of the habitat changes on aquatic animal communities has never been quantified. Small aquatic animals are trophic resources for larger wildlife including wading birds. Over two years we quantified densities of small fishes (< 8 cm, standard length) and large macroinvertebrates with 1-m2 enclosure traps in 12 degraded (sawgrass-filled) sloughs and 12 adjacent remnant sloughs in a paired design within a 14 km2 area of contiguous Everglades wetland where most sloughs had been lost to infilling. Water depth did not differ between the habitats, and the region did not dry to depths (< 5 cm) that would disturb fish populations during or just prior to the years of sampling. Mean total fish (mostly Poeciliidae and Fundulidae) densities and total biovolumes of metaphytic algal mats were higher in the remnant sloughs in all seasons. Aquatic insect densities were 2x higher in the degraded sloughs in the dry season, but did not differ in the wet season. Mean grass shrimp (Palaemon paludosus) densities did not differ by habitat and while crayfish (Procambarus fallax) densities were relatively low overall, the densities were higher in the degraded sloughs. The community composition of fishes and macroinvertebrates also differed between habitats. Our results indicate that degradation of sloughs by sawgrass encroachment has reduced fish densities and suggests that restoration activities focused on rebuilding sloughs could provide significant changes to the trophic functions of the wetland landscape.