Since the exotic Eurasian milfoil Myriophyllum spicatum (L.) was first reported in the Lake Pontchartrain estuary in 1978, it has become established as a dominant species of submerged macrophyte, but its distribution and abundance have varied considerably. We compared fish assemblages among two native macrophytes, Vallisneria americana (Michx) and Ruppia maritima (L.), the exotic M. spicatum, and unvegetated substratum to determine if milfoil influenced assemblage structure and microhabitat use by common littoral fishes. We used a modified Wegener ring to quantitatively assess fish densities. In monthly sampling from March 1991 to January 1993, we collected 3564 fishes of 29 species, but four dominant species, rainwater killifish Lucania parva (Baird), naked goby Gobiosoma bosc (Lacepede), gulf pipefish Syngnathus scovelli (Evermann and Kendall), and clown goby Microgobius gulosus (Girard) accounted for over 87% of the fishes. Community diversity was highest in V. americana, intermediate in unvegetated areas, and lowest in R. maritima and M. spicatum. The patterns for evenness and richness differed from that of diversity among the four habitat types. Analyses of percent similarity and rank correlation of community structure showed no significant differences between M. spicatum and native macrophytes. The common fishes were significantly more abundant in vegetated areas than on adjacent unvegetated substratum, and total abundances were higher in M. spicatum and R. maritima than in V. americana. Only three fishes showed significant differences among macrophyte species: rainwater killifish and clown goby were more abundant in M. spicatum and R. maritima, and bay anchovy Anchoa mitchilli (Valenciennes) was more abundant in M. spicatum than in V. americana. Additionally, fish abundances were related to environmental variables in a factor analysis that resolved nine variables into four axes, characterized in order of importance as: a large-scale spatial (salinity) axis, a seasonal axis, a turbidity axis, and a plant surface area axis. The different patterns of fish species in environmental space revealed spatial and temporal differences in resource utilization. The exotic macrophyte M. spicatum may not have had a detectable influence on fish assemblages or abundances relative to the native macrophytes because high wave energy in the open system may prevent it from growing densely enough to strongly alter microhabitat characteristics.