Transplanted Mytilus galloprovincialis and native Ruditapes philippinarum were deployed in 10 sampling stations with different pollution impact within the Lagoon of Venice to evaluate the temporal variations and the suitability of the following cytochemical and histochemical biomarkers just as indicators of environmental stress: lysosomal membrane stability, lipofuscins, neutral lipids and lysosome to cytoplasm volume ratio. The physiological status of the organisms was also investigated by determining the survival in air capability and the reburrowing rate (clams). The biological parameters were assessed in June and October. Furthermore, for a better definition of the environmental aspects of the study sites, heavy metal, PAH and PCB concentrations were also evaluated in the sediments. As a whole, the biological responses examined in both species from all the sampling sites showed significant differences between the two seasonal campaigns, only lysosomal membrane stability exhibited less variability. Pollutants in sediments generally showed low-intermediate contamination levels, few hotspots persisting mostly in the inner areas of the lagoon, the most influenced by the industrial zone. Transplanted mussels were more responsive than native clams and the biological responses of both species varied temporally. The range of the spatial variability was always narrow and reflected only partially the broader variability shown by the chemical content in the sediments. In this sense, biological responses seemed to be particularly influenced by the high temporal and spatial heterogeneity that characterise the Lagoon of Venice, as well as most of the transitional environments.