Digenean trematodes infecting the mud snail Hydrobia ulvae were studied at two key sites of the Mondego Estuary (Portugal), from January 1993 to September 1995: a mud flat covered by the seagrass Zostera noltii, and a bare sand flat where seasonal macroalgal blooms occurred as a result of eutrophication. Digeneans belonging to Microphallidae, Notocotylidae, Haploporidae and Heterophyidae were recorded in snails from both sites whereas representatives from Echinostomatidae were only found in snails from the seagrass bed. The density of infected snails was higher at the seagrass bed than at the eutrophic area partly reflecting the difference in population structure of H. ulvae between sites. The Zostera noltii bed supports an abundant and well-structured mud snail population, with all size-classes represented, in contrast to a less abundant and juvenile dominated population in the eutrophic area. In the Z. noltii bed no clear seasonal and interannual patterns emerged in the infection densities. In the eutrophic area, the density of infected individuals increased in the presence of algae, and decreased during the occurrence of occasional flood events. Small scale spatial and temporal patterns in the prevalence of digenean trematodes in mud snails were therefore demonstrated within the Mondego Estuary that has experienced a mixture of anthropogenic impact and climate instability.