In addition to the statutory designations at several of the lakes, many have areas set aside as Special Protection Zones or Nature Reserves. These areas are deemed internally as high quality conservation value and do not have any recreational activities taking place within them with the exception of footpaths for walkers.
The zones vary in size and composition, but the aim is to protect the valuable habitats and species within them.
| Site | Location | Area (hectares) | Feature |
| Argal | Southern end | 3 | Semi-natural and planted broadleaved woodland, including areas of rich bryophyte flora, and wet woodland |
| Burrator | Eastern arm | 14.16 | Wet woodland |
| College | Whole site | Wet woodland, willow carr, inundatio n vegetation, broadleaved plantation, otter, bats | |
| Colliford | Loveney Reserve (Northern half of the eastern arm) | 161.88 | Original moorland, abandoned semi-improved pasture, marshy inlets with feeder streams lined with willow carr, an island meadow bordered by an excavated moat and a variable shoreline. |
| Drift | Majority of site | 59 | Species-rich meadows, wet woodland |
| Fernworthy | South eastern arm | 8 | Purple-moor grass, meadows, woodland plantation, marsh fritillary |
| Kennick | Smithacott (North) | 0.81 | Marsh, damp woodland, rich marginal vegetation, pied flycatcher, otter |
| Meldon | South western end | 5.79 | Dry heathland, island acting as wildlife refuge, Porth Eastern end 24.69 Semi-natural broadleaved wooland, willow carr, swamp, otter |
| Stithians (2) | Northern cut off and southern arm | 6 | Rough pasture, willow carr, bog and wetland, heathland and the littoral zone, |
| Lower Tamar | Whole site | 27.92 | Wet woodland, otter |
| Wimbleball | Hurscombe Nature Reserve - northern arm | 18.62 | Purple-moor grass & rush pasture, hedgerows, pearl-bordered fritillary |
| Wistlandpound | North eastern arm | 1.62 | Broadleaved woodland, marginal vegetation, standing water, scrub, otter, willow tit, lichens & mosses |
Each year, the Trust produces a written summary of the management and wildlife sightings within each reserve for South West Water.