The Marine shelf biome is distributed globally between the shoreline and deep sea-floor biomes and is dominated by benthic productivity. It includes ecosystems with biogenic substrates (such as seagrass meadows, kelp forests, oyster beds, and coral reefs) and minerogenic substrates including rocky reefs, sandy bottoms, and muddy bottoms.

The availability of light and nutrients are key structuring factors, influencing productivity and ecosystem structure and function. Turbidity and depth gradients influence light availability. Productivity depends on upwelling currents that deliver nutrients from the deep ocean floor as well as the strength of nutrient inputs from the land, delivered largely by fluvial systems. Light is influenced by depth gradients but also by water clarity (cf. turbidity) and determines whether macrophytes and animals dependent on photosynthetic symbionts are able to establish and persist.

Additionally, whether the bottom type is hard or soft dictates whether sessile organisms can dominate, forming biogenic habitats that protrude into the water column. A shallow water biome, the marine shelf is shaped by kinetic wave energy and, in polar regions, also ice scour. Positive feedback loops, whereby the habitat structures formed by sessile organisms dampens kinetic energy, can enable ecotypes to persist under marginally suitable conditions. The strength of top-down control by consumers can be an important factor in determining community structure.

Depending on the benthic biota, energy sources can vary from net autotrophic to net heterotrophic. Temperature and (to a lesser extent) salinity influence the presence and identity of dominant habitat-forming biota. Currents can influence ecotypes by determining patterns of larval dispersal and the flow of resources.