This study examined the relationship between urbanization and parasite community structure in the estuarine fish, Fundulus heteroclitus. We measured landscape and physicochemical factors associated with urbanization at 6 sites from 4 collection periods. Concurrently, we quantified the metazoan parasite community in F. heteroclitus collected at those sites, with 105 fish studied per site during the 4 collection periods. Parasite community composition differed among sites. Host size was the most important variable for direct life-cycle parasite assemblages and indirect life-cycle parasites at the individual fish level, while landscape and physicochemical factors determined the structure of indirect life-cycle parasite assemblages at the population scale. Variation in the prevalence and intensity of infection of two indirect life-cycle parasites, Lasiocotus minutus and Glossocercus caribaensis, were the primary parasites that drove differences across sites. Variation in the presence/absence of these indirect life-cycle parasite species was associated with sediment Ni concentrations, patch density, and marsh size. Our data support the hypothesis that urbanization, acting at both landscape and physicochemical scales, can have a significant impact on parasite community structure. This, however, varied by parasite life history: there was little effect of urbanization on the prevalence and intensity of direct life-cycle parasites, but significant variation was detected for indirect life-cycle parasites. This study demonstrates how anthropogenically driven landscape change influences fine-scale population dynamics of parasites.