The Deben Estuary is designated under various national and local schemes as a Site of Special Scientific Interest; Special Protection Area; under the Ramsar International Convention on Wetlands and as part of the Suffolk Coasts and Heaths Area of Outstanding Natural Beauty (AONB).

Over the 12 km covering the tidal stretch of the Deben between Felixstowe Ferry at the mouth of the river and Wilford Bridge north of Woodbridge,  the landscape of the estuary ranges through coastal levels, saltmarsh and intertidal flats to estate sandlands.  Use the “+” feature on the interactive map of landscape types in Suffolk to zoom in on the Deben.

The Estuary is relatively narrow and sheltered, and has limited amounts of freshwater input. The estuary mouth is the narrowest section and is protected by the presence of shifting shingle banks or knolls. The intertidal areas are constrained by sea walls.

The saltmarsh and intertidal mudflats that occupy the majority of the area display the most complete range of saltmarsh plants in Suffolk (suffolk saltmarsh).

A range of freshwater marsh communities fringe the estuary, and occasionally form larger stands. In general, these are dominated by Common Reed.

A partnership of local voluntary and statutory organisations, the Deben Estuary Partnership, was set up to create management partnerships to safeguard the estuary from degradation. After local consultation, in which the River Deben Association was involved, a comprehensive plan, the Deben Estuary Plan,  which deals with all aspects of the river and its environs,  was published in April 2015.