Marine ecosystems are increasingly affected by climate change and eutrophication, placing considerable stress on macroalgae and potentially disrupting their mutualistic interactions with surface-associated microorganisms, especially bacteria. This study explored the temporal dynamics of epiphytic microbial communities (16S rRNA) and the surface metabolome (LC-MS) of Ulva spp. from southern Brittany (France) over a 17-month period. The data obtained were analyzed through multivariate techniques to uncover correlations between bacterial community structure and surface metabolites. Biochemical and environmental parameters were also examined to identify the factors driving temporal variations in the macroalgal surface landscape. The analysis revealed distinct bacterial communities on Ulva spp. surface, compared to those in surrounding seawater or on rocky substrate. Key environmental factors, including salinity, nitrate concentration, and precipitation, as well as the physiological traits of Ulva spp. (such as uronic acid content, lipid levels, and moisture), were identified as primary drivers of microbiota dynamics. A stable core microbial community, primarily composed of Alphaproteobacteria, Flavobacteriia, Oligoflexia, and Saprospira, was also observed within the Ulva spp. microbiota. Finally, correlations between Amplicon Sequence Variants (ASVs) and surface metabolites underscored the importance of an integrated multi-omics approach to enhance our understanding of the complex dynamics between eukaryotic hosts and their associated microbiota.