The forest habitats of the Tahoe basin have been significantly impacted by human activity since European discovery in 1844. During the period from 1870 to 1890, many of the forests in Tahoe were clearcut to be used as firewood, shoring for mines, and homes in support of the Comstock mining operations in Virginia City. In particular, large old growth trees which can take 300 to 400 years to grow back were cut down. Fire, which was an important natural process in the forests, has been eliminated over the past hundred years in response to a nation-wide policy of aggressive fire suppression. As a result, today's forests are less structurally diverse and support fewer wildlife species, including many sensitive species.

The Forest Ecology program focuses on restoring the forested habitats of the Tahoe Basin through direct implementation of projects on Conservancy property. These projects are designed to improve habitat, reduce fire threat, and promote natural processes through the reintroduction of prescribed fire, thinning of conifer and aspen stands, and road obliterations.

Recognizing its importance in naturally functioning forests, prescribed fire is being emphasized to restore habitat diversity by creating a mosaic of vegetation types and ages. Fire also reduces the threat of wildfire by consuming understory vegetation and ground fuels. However, important habitat features such as snags, logs, and large trees, are protected prior to conducting burns.

Removal of trees is sometimes needed to restore forest structure. In conifer stands of pine and fir, this is accomplished through the use of equipment or hand crews. The overall density of a stand may be reduced in order to allow for regeneration of understory trees, allow remaining trees to grow better, and to allow for the safe reintroduction of fire. Conifers may be removed from aspen stands by hand crews in order to enhance this critical habitat type.

Since the beginning of its efforts in 2000, the program has implemented one fuels reduction project in the Kings Beach area and is planning a number of habitat enhancement projects on the north, west, and south shores of the lake.