Murray observed that Loch of Harray is a freshwater loch, the largest in all Orkney with an area of approximately 3.75 square miles (9.7 square kilometres) and volume of 951,000,000 cubic feet (0.0269 km3) and that it is somewhat influenced by the tides in the Hoy Sound although there is little variation in its level.

Murray recorded that despite there being an inlet allowing the free flow of water from the Loch of Stenness it has little impact on the biology of Harray and no seaweed was present, the water tasted fresh and normal freshwater plankton were seen.

[7] The loch is a Site of Special Scientific Interest and has a large number of pondweed species three of which are scarce, a rare caddis fly (Ylodes reuteri) and is the only known site in Scotland for a nerite snail Theodoxus fluviatilis which is more commonly found in English rivers.

A wide variety of wildfowl winter at the loch including pochard, tufted duck, scaup and goldeneye.

[8][9] It has been designated an Important Bird Area (IBA) by BirdLife International because it supports populations of waterbirds.