Abstract
Microbial communities underpin ecosystem processes and biogeochemical cycles in marine ecosystems, yet their spatial and temporal dynamics at hourly scales remain poorly understood. We surveyed two stations from the North Sea (NS) and Wadden Sea (WS), generating six high‐frequency time‐series datasets across depths and seasons, complemented by sediment cores. Across seasons, the sites in the NS and the WS harbored distinct microbial communities shaped by contrasts in salinity, temperature, and potentially the quantity and lability of organic matter. Connectivity between communities was limited but favoured by known seasonal hydrographic exchanges. Despite taxonomic contrasts between sites, functional turnover remained low, with communities harbouring similar metabolic potential but being adapted to local conditions, suggesting potential functional redundancy. At hourly scales, community turnover was weaker and largely driven by vertical and horizontal mixing between water masses, occasional resuspension from sediments, or a summer bloom from a copiotroph. These shifts were transient and did not disrupt the coupling between taxonomic and functional composition. However, their immediate effects on ecosystem processes, such as organic matter remineralisation and nutrient recycling remain unclear. Continued high‐resolution microbiome monitoring, paired with biogeochemical flux measurements, is needed to better predict climate‐driven changes in coastal ecosystem functioning.