Estuaries are coastal inlets where, unlike 'large shallow inlets and bays' there is generally a substantial freshwater influence. Pembrokeshire European Marine Site includes the Daugleddau estuary and also smaller estuaries entering the Daugleddau and Milford Haven such as the Pembroke River, Cosheston Pill, Carew and Cresswell Rivers, Garron Pill, Sprinkle Pill, and Millin Pill to name the most prominent.

The wide range of environmental conditions, particularly seabed substrata, tidal streams and salinity gradients, support a wide diversity of both communities and numbers of species. The species richness of sediment animal communities throughout Milford Haven and the Daugleddau is high. Intertidal mudflats draining into the main Waterway support rich and productive shellfish and worm communities. Muds typically support a greater biomass than other intertidal sediments. The abundant intertidal sediment infauna is an important food source that supports large numbers of overwintering waders and wildfowl.

Shell/cobble substrates and bedrock in the upper reaches of the Daugleddau are particularly spectacular with huge colourful anemones, sprawling current-swept sponges and carpets of sea squirts.