The coastal or nearshore bottoms of freshwaters and oceans play an important role in governing ecosystem processes. The sediments support important biogeochemical transformations from land to water, contribute to emissions and sequester greenhouse gasses, provide critical habitats for native biodiversity, and can mediate the trophic transfer of contaminants. Recent, observations reveal unexpected changes to the bottoms habitats of relatively pristine freshwater and marine systems. For example, large, clear lakes with exceptional water quality (Tahoe, Baikal, Wakatipu and Taupō) have recently experienced filamentous algal blooms. In marine ecosystems, coastal darkening is expanding; the controls on these processes are not well understood. Across these aquatic biomes, one thing is increasingly certain, the commonly applied knowledge derived from open-water habitats does not apply to the observed changes along the nearshore and coastal bottom habitats. In this session, we explore process-based connections that lead to altered nearshore bottom environments across freshwater to marine biomes.