The wildlife of the Lunan Lochs reflects their special quality.
With several rare species, shallow, clear water and a wide range of wetland habitats the lochs hold a special place within the broad biodiversity of the Scottish landscape and warrant continued protection and management. All five lochs: Craiglush, Lowes, Butterstone, Clunie and Marlee have been designated as Sites of Special Scientific Interest (SSSI's) and together are one of only 230 sites in Scotland which have been put forward to become a special area of conservation (SAC) - a wildlife site of European importance.

Birds
Osprey, have been breeding adjacent to Loch of Lowes since 1969, despite egg thieves. Their arrival each Spring signifying their place at the top of the food chain as they feed on the healthy fish populations of the lochs.
Greylag Geese use the lochs and surrounding land as a roost and the lochs form part of an important network of goose roosts in the Tay-Isla valley.
On the lochs can be seen a rich variety of wildfowl, with breeding colonies of Slavonian Grebe, Little Grebe, and Great Crested Grebe. Teal and Tufted Duck are also known to breed.

Mammals
Otter in particular have a steadily increasing population since their decline in the 1960's and 1970's. Using the Lunan Burn as secure passage from loch to loch. Occasionally they can be seen from the hide on Loch of the Lowes.
A total of thirty-three mammals have been recorded in the area. Including, Badger, Red Squirrel, Wild Cat, Pine Martin and Pipistrelle Bat. With Reptiles, Slow Worm, Adder, and Common Lizard also recorded.

Invertebrates include notable examples of water beetle and in Loch Marlee water weevil Eubrychius velutus. Unfortunately, pearl fishing is blamed for the virtual demise of the rare Freshwater Pearl Mussel Margaritifera margarritifera, which was recorded as occurring as far back as 1860 in the Lunan Burn. The Lunan Burn has had very little disturbance and many river habitats still survive the more typical canalisation seen on lowland rivers throughout Scotland.
 

Plantlife
The lochs have an exceptional range of aquatic flora particularly several species of pondweed and a number of locally and nationally rare plants. These alone make the lochs of international importance. The Fen areas fringing the lochs are also of considerable botanical interest, supporting a wide range of species. On Loch Marlee eleven species of Sedge have been recorded.
One plant, the Slender Naiad Najas flexilis is especially rare. The Lunan Lochs considered to be one of only four remaining localities in the UK.
The Slender Naiad is a delicate water plant (see right) which grows submerged in only a few areas of Scotland, notably in the machair lochs of the Outer Hebrides. It is threatened over much of Europe and no longer occurs in England.
Water quality and environmental conditions are extremely fragile and susceptible to pollution and nutrient enrichment, careful monitoring is required. Particularly sensitive to water quality is the Slender Niad and as such can be an early warning indicator of any potentially harmful effects such as pollution.