We examined patterns of habitat use by fishes and decapod crustaceans in a seemingly pristine tidal stream system that drains into southeastern coastal Louisiana, northern Gulf of Mexico. The study area centered on a relatively unaltered mesohaline saltmarsh nested within more heavily degraded conditions. Monthly sampling (February–November 2004) stratified along a stream-order gradient examined changes in nekton abundance, species richness, and community structure. Analyses were based on a microhabitat approach used to characterize nekton responses to spatial gradients of water depth, temperature, dissolved oxygen, salinity, turbidity, bottom slope, stream width, and distance to mouth. Thirty taxa were identified from 3,757 individuals collected in 82 seine samples. Seven fishes and three decapods constituted >95% of the community structure. Analyses detected the effects of stream order on fish community structure and associated environmental variables. Spatial differences of environmental variables across stream order were attributed to the geomorphology and hydrology of the study area. A factor analysis resolved eight environmental variables into four orthogonal axes that explained 80% of environmental variation. We interpreted factor 1 as a stream-order axis, factor 2 as a morphological axis, factor 3 as a seasonal axis, and factor 4 as a salinity axis. Differences in use of four-dimensional factor space by dominant species reflected habitat selection and species residency status.