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Cerastoderma edule (edible cockle) is among the most exploited bivalves in Europe playing an important socio-economic role. Cockles live in estuaries and lagoons where their population is controlled by several environmental factors including parasitism. Parasites represent an important part of the world known biodiversity but are often neglected. Trematodes are the most prevalent macroparasites of cockles being able to exert an impact both at the individual and population levels. Therefore, it is of prime relevance to recognize and understand the parasite-host system dynamics in order to better predict potential conservation threats to bivalve populations and to maximize the success of stock and disease episodes management.Cockle monitoring was conducted in 2012 and 2016, in six and eight stations, respectively, at the Ria de Aveiro coastal lagoon, Portugal. Cockles were sampled in one single occasion in 2012 and seasonally in 2016. The tested hypothesis is that the trematode community in cockles was spatially and seasonally heterogeneous but stable over time. The main result showed that despite a relative homogeneity of the parasite community structure in cockles, the among-years heterogeneity of trematode communities was higher than among-stations and among-seasons heterogeneity rejecting the postulated hypothesis. Results demonstrated that trematode communities from the Ria de Aveiro are characterized by low abundance, which resulted in a spatial and seasonal trematode homogeneity (despite an overall channel difference and a slight downstream-upstream gradient). The interannual analysis showed a worrisome loss of trematode diversity and prevalence which consequently indicates an important loss of overall diversity and/or environmental conditions reflecting the negative effects of global change (mean temperature rise and overharvesting, among others). The present study highlighted the importance of trematodes in characterising their associated environment and respective biodiversity which might be helpful to assess ecosystem ecological status and to identify threatened areas.Trematode communities from the Ria de Aveiro are characterized by low abundance.Trematode communities showed to be spatially homogenous and showed no seasonal pattern.Interannual differences in trematode parasite community structure were detected.Trematode communities can be used as early warning indicators of global changes.Effective use of trematodes to assess ecosystem's deteriorating conditions.