The occurrence of trematodes within the gastropod Hydrobia ulvae was studied in two areas (a Zostera noltii bed and a eutrophic area) in the Mondego Estuary, Portugal. The aim was to assess trematode infections across snail age classes, as well as to investigate any influence of parasitism on the shell shape and size of these gastropods. In the Z. noltii bed, infection occurred in snails with shell height of 1.5–6 mm, but a higher prevalence was seen in intermediate size classes (3–5 mm). Infected individuals were never found among the elder gastropods. In the eutrophic area, infection was commonly observed within small individuals (1.6–2.5 mm), as large individuals were rarely found. The warm temperate climate in this coastal system may cause infected specimens to die before they can grow to larger dimensions, in contrast to Northern European populations. The frequency of snails with thin, distorted and corroded shells was higher among infected than non-infected snails. Infected individuals were frequently colonized by epibionts that may have additional detrimental effects and probably promote shell erosion. Infection with trematodes and their influence on snail size needs consideration in the evaluation of parameters related to population dynamics and population structure. If the implications of parasite infection are ignored, inadequate decisions about ecosystem management may be taken, resulting mainly from erroneous assessment of population structure, age composition and ecological longevity. The role of parasites is especially important to consider for systems under environmental stress.