The Jewel in the ecological crown of Hoo St Werburgh is the magnificent Medway Estuary and Marshes. Seen from the foreshore the estuary forms a single tidal system with the Swale and joins the southern part of the Thames Estuary between the Isle of Grain and Sheerness forming the Northern section of the renowned North Kent Marshes.
The site has a unique complex arrangement of tidal channels, which drain around large islands of salt marsh and peninsulas of grazing marsh. There are large areas of mudflat, which have high densities of invertebrates providing a good food source for wading birds. Grazing marsh can also be found landward of some sea walls in the area. Small shell beaches occur too, particularly in the outer parts of the estuary. The area is very flat and low lying, with large expanses of uninterrupted views.
The complex and diverse mixes of coastal habitats support important numbers of waterbirds throughout the year. In summer, the estuary supports breeding waders and terns, whilst in winter it holds important numbers of geese, ducks, grebes and waders. The middle and outer parts of the estuary represent the most important areas for the birds. Important areas for birds include the Saltings and Hoo flats on the north side and the stretch from Copperhouse marshes eastwards towards Chetney marshes on the south side. The islands within the Medway also provide good habitat for protected birds, in particular some of the breeding species. The two main protection designations are the Medway Estuary and Marshes Ramsar site and Medway Estuary Marine Conservation Zone. These the whole foreshore and intertidal habitats from Upnor to Grain (and beyond) and across the medway to Gillingham and Rainhan and on to the Swale.