The Transitional waters biome includes coastal inlets that are influenced by inputs of both fresh and marine water from terrestrial catchments and ocean tides, waves, and currents. They include deep-water coastal inlets or fjords mostly restricted to high latitudes, as well as estuaries, bays, and lagoons, which are scattered around coastlines throughout the world.

Gradients in water regimes, water chemistry, depth, temperature, size, and salinity influence the function, productivity, diversity, and trophic structure of these transitional ecosystems. The balance between marine or freshwater influences varies seasonally and inter-annually depending on the climate and among inlets with differing geomorphology, catchment size, climate, and exposure to waves and currents. In some cases, ecosystems characteristic of the marine shelf biome (e.g. M1.1 Seagrass meadows) may have significant occurrences within semi-confined transitional waters. Some inlets are permanently connected to the ocean but others are only intermittently connected, influencing exchanges of water, nutrients, and biota among ecosystems. The dynamics of connection and closure of shallow inlets are regulated by variations in stream flow inputs and wave activity.

Strong horizontal and vertical salinity gradients (varying with freshwater and marine inputs) structure biotic communities and traits that equip species for occupying different salinity niches. Autochthonous energy generated by primary production from aquatic macrophytes, phytoplankton, macroalgae, and diatoms is subsidised by allochthonous inputs from inlet shorelines, freshwater streams, and marine incursion. These high levels of energy availability support complex trophic networks, including large populations of macroinvertebrates, fish, waterbirds, seabirds, and some mammals and reptiles. Many inlets function as fish nurseries and bird breeding sites.