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This Special Issue explores the assessment of benthic biodiversity, spanning microbes, protists, megafauna, and fish, and its responses to both natural and human-induced drivers. It emphasizes how these communities influence key ecosystem functions such as biogeochemical fluxes and material transport across the seafloor. Despite advances in marine ecology, much of the benthic realm—particularly beyond macrofauna—remains poorly understood. By bringing together observational, experimental, and modeling approaches, this collection provides new insights into the complex dynamics of benthic communities and their reactions to environmental gradients and anthropogenic pressures.