Muddy subtidal sediments in the Belgian Coastal Zone (BCZ, southern North Sea) are characterized by high concentrations of trace metals. During spring, this area is characterized by extensive phytoplankton blooms, which upon sedimentation induce intense remineralization and significant changes in the redox state of the sediments, leading to enhanced trace metal effluxes. We used microcosms to evaluate the interaction between the deposition of moderate concentrations (+ 7.1 mg m-2 of chlorophyll a) of the diatom Skeletonema sp. and the haptophyte Phaeocystis globosa, metal effluxes and microbial community structure and activity. Sediments were sampled after 0, 2 and 7 days. Changes in composition and activity of both the bacterial and microbial eukaryotic communities (with emphasis on Protozoa) were analyzed using molecular methods (16s and 18s rDNA and rRNA extractions followed by DGGE), and related to bacterial biomass, number of heterotrophic nanoflagellates, dissolved metals and other geochemical variables (redox, 02, salinity, pH, chlorophyll and DOC). Gamma-Proteobacteria, Bacteroidetes and delta- Proteobacteria were the dominant bacterial members, while Alveolata (ciliates, dinoflagellates and apicomplexans), diatoms, Fungi, and Amoebozoa were dominant in the microeukaryotic communities. DNA- and RNA-based fingerprints of bacteria and Protozoa showed distinct changes in the total and active community structure as a consequence of the algal enrichment, and with time. The enrichment effect was most pronounced after 2 and 7 days for bacteria and Protozoa respectively. Our results suggest that phytodetritus deposition activates and stimulates the microbial loop, via changes in bacterial activity, biomass and community composition, together with subsequent changes in numbers and relative abundance of heterotrophic nanoflagellates and ciliates, and composition and activity of protozoan communities.