Many coastal habitats worldwide are anthropogenically developed (transformed) at such a rate that they experience negative impacts from human activities. These include nutrient inputs within and among estuaries with varying levels of anthropogenic influence depending on flushing time. These impacts may affect species interactions (including host-parasite) and health in estuarine marsh habitats. The condition of organisms, such as eastern mud snails (Ilyanassa obsoleta), can be an indicator of the quality of these ecosystems, and their degree of anthropogenic influence. Snails, sediments, and water samples were collected from two different conservation areas in a small, highly eutrophic estuarine system along the east coast of the United States (Barnegat Bay, New Jersey). Both areas are designated as protected; one is in an area just north of one of three main inlets that provide ocean access to the estuary, and the other is to the south of the inlet. Condition of the mud snails was determined by length and thickness of the snail shell, snail total weight, and presence of epibiosis (visible algae on snail shells), as well as the number of cysts of the parasitic trematode Pleurogonius malaclemys. Overall, the sediment and water qualities were better in the southern area than in the northern area. In the summer months, snails at both areas were significantly heavier, with thicker and longer shells. There was a significantly higher prevalence of P. malaclemys cysts found on the snails, and thinner and shorter snail shells in the northern area, which can be attributed to the degraded environmental conditions. This bottom-up study utilizes I. obsoleta as an indicator organism to exemplify the repercussions of human intrusion on the state of estuarine ecosystems, which is a microcosm for global estuarine health. Our results show that the location of conservation areas is key to the quality and effectiveness of these areas, especially with regard to seasonal changes.