The nature reserve is managed primarily for bird conservation, particularly through control and improvement of wetland, heath and grassland habitats, with particular emphasis on encouraging nationally uncommon breeding species such as the bittern, stone-curlew, marsh harrier, nightjar and nightingale. The diversity of habitats has also led to a wide variety of other animals and plants being recorded on the site.
Before becoming a nature reserve, the area was the site of an ancient abbey and a Tudorartillery battery. The marshes were reclaimed as farmland in the 19th century, but were re-flooded during World War II as a protection against possible invasion.
The reserve has a visitor centre, eight bird hides and an extensive network of footpaths and trails. Entry is free for RSPB members. Potential future threats to the site include flooding or salination as climate change causes rising sea levels, coastal erosion and possible effects on water levels due to the construction of a new reactor at the neighbouring Sizewell nuclear power stations.
The area around Minsmere consists of the wide valley of the Minsmere River with Dunwich cliffs to the north and Sizewell cliffs to the south. Two extensive sandbanks lie off the coast, and the beach is sand overlain with shingle. The cliffs have a maximum height of about 17 m (56 ft) and are amongst the most rapidly eroding in the UK, at an annual rate of 1–2 m (3.3–6.6 ft).
From 500 BC to 700 AD, the sea level in Suffolk was about 6 m (20 ft) higher than it is today, and the low-lying areas of the present coast were then tidal estuaries. The river mouth was finally closed in the 18th century as sand and shingle deposits formed off the coast. The higher land consists of a deep layer of gravel and sand, the legacy of the beach formed by the sea before it retreated. The geology of the wetland areas below the topsoil is marine clay with darker freshwater deposits from the Minsmere River.