Marine mucilage has been described as worldwide phenomena occurring sporadically, or frequently in certain coastal areas. They are transitory phenomena that can remain in the photic zone for several days or weeks. Their occurrence has been more frequent and persistent, and their magnitude has increased during the last decades. Their formation typically reflects an imbalance in the marine microbial communities, and has frequently be linked to global changes. Recurrent marine mucilage events have been observed in recent years in the Southern Bay of Biscay near the French coast, mainly south of the Adour estuary. In this study, we used a fingerprinting method (T-RFLP) targeting 16S and 18S rRNA genes to investigate marine microbial community composition and dynamics over an annual cycle across the three domains of life in coastal water at three depths, in the Adour River upstream of the mouth and in the marine mucilage. In line with studies conducted in marine environments we highlighted that the dynamics of marine microbial communities in the Bay of Biscay coincided with two environmental contexts: winter and spring on one hand and summer and autumn on the other hand. More interestingly, this dynamics affects also the marine pelagic mucilage that was observed during the sampling campaigns. Thus, the composition of the marine mucilage that appears in winter/spring context diverges from the composition of the marine mucilage that occurred during the summer/autumn context. We highlighted also that marine microbial communities were partly different from marine mucilage communities with an enrichment of some microorganisms suggesting that marine mucilage behaves as a microhabitat in seawater and possesses distinct microbial assemblages from the surrounding communities.