As the production of cultured bivalve mollusks is increasing worldwide, there is a growing need to study the biodiversity and ecology of microalgae in the mariculture zones. This study presents multiannual data (obtained in 2015–2016 and 2018–2020) on the species composition, abundance, biomass, and community structure of microphytobenthos from three mussel farm ecotopes (mussel shells, the epiphyton of twenty macroalgal species, and sediments under collectors). In total, 150 microalgal taxa were found, including 135 diatom species with a predominance of benthic (76%), marine (65%), and cosmopolite (30%) ones. In all habitats, 10 potentially harmful species and 44 indicators of organic pollution were noted. The maximum values on the mussel shells (abundance N = 119 × 103 cells/cm2 and biomass B = 0.0489 mg/cm2) were recorded in winter with the dominance of Tabularia fasciculata; in summer, the epiphyton was on the brown alga Nereia filiformis (N = 1001 × 103 cells/cm2 and B = 2.06 mg/cm2) with the dominance of toxic Pseudo-nitzschia seriata, on the red alga Phyllophora crispa (N = 1118 × 103 cells/cm2 and B = 3.24 mg/cm2) with the dominance of T. fasciculata, and in sediments (N = 104 × 103 cells/cm3 and B = 0.046 mg/cm3) with the dominance of T. fasciculata and Bacillaria paxillifer. Statistically significant effects of the ecotope and sampling season on the diatom composition were noted. The strongest effect of temperature is observed for the mussel shell diatoms, for which the trend of abundance and biomass increase in winter and their decrease in summer is most noticeable. But in sediments, the effect of the season is reflected only in the permanent changes of the microalgae species composition. For the epiphyton, it was shown that it is temperature, rather than substrate macrophyte species, that affects its numerical structure.