Carpet shell clam populations on the Tunisian coastline are susceptible to several microbial pathogen challenges. In this study we report the results of five years' surveillance, conducted from January 2004 till June 2009, for detection of Perkinsosis and brown ring disease (BRD). The survey covered three sites of natural populations of Ruditapes decussatus in a Tunisian lagoon, the North Lake of Tunis. Perkinsosis was detected preferentially in winter periods from the external and marine site, BRD was detected more frequently in the summer periods in a more proximal collection site (in the lake) and was positively correlated with concentrations of heterotrophic Vibrio sp. Our results suggest that several factors other than temperature and salinity might explain spatial distribution variability and natural intensities for these infections in carpet shell clam populations.