Tropical cyclones can severely disturb shallow, continental shelf ecosystems, affecting habitat structure, diversity, and ecosystem services. This study examines the impacts of Hurricane Ian on the Southwest Florida Shelf by assessing water quality, substrate type, and epibenthic and microbial community characteristics at eight sites (3 to 20 m in depth) before and after Ian’s passage in 2022. Hurricane Ian drastically changed substrate type and biotic cover, scouring away epibenthos and/or burying hard substrates in mud and sand, especially at mid depth (10 m) sites (92–98% loss). Following Hurricane Ian, the greatest losses were observed in fleshy macroalgae (58%), calcareous green algae (100%), seagrass (100%), sessile invertebrates (77%), and stony coral communities (71%), while soft coral (17%) and sponge communities (45%) were more resistant. After Ian, turbidity, chromophoric dissolved organic matter, and dissolved inorganic nitrogen and phosphorus increased at most sites, while total nitrogen, total phosphorus, and silica decreased. Microbial communities changed significantly post Ian, with estuary-associated taxa expanding further offshore. The results show that the shelf ecosystem is highly susceptible to disturbances from waves, deposition and erosion, and water quality changes caused by mixing and coastal discharge. More routine monitoring of this environment is necessary to understand the long-term patterns of these disturbances, their interactions, and how they influence the resilience and recovery processes of shelf ecosystems.

Microbial communities play a crucial role in coastal ecosystem function, yet their seasonal and spatial dynamics in response to environmental change remain underexplored in tropical and subtropical regions. This yearlong study investigated microbial composition in water, sinking particles, and sediments along an inshore–offshore gradient influenced by the Caloosahatchee River Estuary in southwest Florida. The region has been altered by rapid coastal development and was struck by Hurricane Ian in September 2022. Environmental parameters exhibited significant spatiotemporal variation, shaping microbial beta diversity in all habitats. Sediment communities showed the greatest hurricane-induced disruption but returned to pre-disturbance conditions within six months. Dominant microbial classes included Alphaproteobacteria, Bacteroidia, and Gammaproteobacteria. Biogeochemical cycling taxa displayed strong habitat specificity, such as Desulfobulbia which dominated sinking particles, Desulfobacteria which was abundant in sediments, and Nitrosomonadaceae and Nitrosopumilaceae which were key nitrifiers in water and sediments, respectively. Particle–sediment taxonomic overlap suggests resuspension processes. Several inshore microbial indicators were consistently present across microbial habitats, especially at estuarine sites, suggesting the estuary as a microbial diversity reservoir for the coastal zone. These results highlight the value of long-term microbial monitoring to understand ecosystem change and resilience in dynamic coastal environments.