It lies about 3 miles to the south of Llangefni and is accessible off the A5 road just to the northwest of the village of Pentre Berw. The reserve can be viewed from the Lôn Las Cefni path/cycle path, and a number of footpaths cross the site. The marsh is a Site of Special Scientific Interest (SSSI), with the north eastern part comprising an RSPB reserve.

Particular priorities here are to manage the habitats for breeding lapwing and bittern. The unmistakeable booming calls of male bittern were once commonplace, and whilst these secretive reedbed specialists frequently over-winter here, the hope is that they will stay to breed. The marsh supports large numbers of breeding birds, which includes snipe, redshank, curlew, reed bunting, tufted duck, shelduck, shoveler, mute swan, and at least four species of warbler; grasshopper, sedge, reed and Cetti’s. Buzzards and kestrels also breed and possibly marsh harriers. Summer visitors include black tailed godwit and ruff.

The marsh is a vital feeding area for migrating and wintering waders and wildfowl, including the area’s important pintail population. The extensive reedbed and system of marshes, wet grassland and lakes and pools supports an incredibly diverse flora. Dominant species include reed canary-grass, water-plantain and branched bur-reed, as well as the locally important reed sweet-grass, horned pondweed, flowering rush, water violet, mare's tail and marsh stitchwort. The nationally scarce pillwort and autumnal starwort also occur. The reserve has a rich assemblage of dragonflies and damselflies, including three nationally scarce species: the hairy dragonfly, the variable damselfly and the scarce blue-tailed damselfly. Malltraeth Marsh is notable as one of north west Wales’ most important sites for the increasingly scarce water vole.