Very few studies have characterized the concentrations of pollutants in bioturbating species. These species are considered as ecosystem engineers and characterizing stressors, such as contaminants, that impact them could lead to a better understanding of the functioning of ecosystems. In addition to contaminants, bioturbators are affected by a wide range of stressors, which can influence their physiological status and their ability to accumulate pollutants. Among these stressors, parasitism is of particular concern due to the ubiquity of parasites in natural environments and their influence on the fitness of their host. This study aims to assess the relationship between parasitism and metal accumulation in the bioturbating mud shrimp Upogebia cf. pusilla. A one-year seasonal survey was conducted in Arcachon Bay, France, with the aims of (1) characterizing the levels of metals in the mud shrimp and (2) evaluating the influence of two macroparasites (a bopyrid isopod and a trematode) on the variation of the metal content in mud shrimp. The bopyrid parasite castrates its female host and a particular attention has therefore been paid to the reproductive cycle of female mud shrimp by quantifying the expression of the vitellogenin gene that encodes the major yolk protein in female crustaceans. The levels of contaminants in mud shrimp appeared low compared to those reported in other crustaceans in areas of higher pollution. Even at these low contamination levels, we observed a significant impact by the bopyrid parasite that depends on season: bopyrid-infested organisms are generally more contaminated than their uninfested conspecifics except in summer when the opposite trend was observed. We suggest that the bopyrid indirectly interferes with the metal accumulation process by altering the reproductive capabilities of the mud shrimp. On the opposite, very low influence of the trematode parasite on the metal content of the host was found.