The Rivanna continues southeast through Fluvanna County, passing the communities of Lake Monticello and Palmyra; it enters the James River at the town of Columbia.

One in particular, a mound postulated to be the site of ritual burial and of spiritual significance to the tribe, is located near the confluence of the two forks of the river and was documented by Thomas Jefferson in his 1781 work Notes on the State of Virginia.

Shortly after the completion of the initial Rivanna navigational works, Virginia requested that the river be opened to public usage.

It now takes hikers all the way around Charlottesville, passing through many of the city's parks and the wooded lands surrounding it, totaling over 20 miles (32 km) in length.

In 2001, The Nature Conservancy, noting its many endemic and rare species including the endangered James River spinymussel, identified the Rivanna basin as “one of the finest remaining freshwater river and stream systems in the Piedmont.” In 2002 a local scientist, John Murphy, founded a community-based monitoring program named StreamWatch.

In 2008 the Rivanna River Basin Commission Technical Advisory Committee identified altered hydrology and sediment pollution as principal threats to the health of the system.

Subsequently, however, some citizens have criticized the plan on the basis of cost, and have encouraged further research about dredging the South Fork Rivanna Reservoir.

The Rivanna River Basin Commission and the community monitoring program (StreamWatch) feature substantial participation by citizens, the conservation community (e.g. Rivanna Conservation Alliance), local governments (Albemarle County, Fluvanna County, Greene County, and the City of Charlottesville), resource management agencies (Virginia Department of Environmental Quality, Virginia Department of Game and Inland Fisheries, Thomas Jefferson Soil and Water Conservation District) and quasi-governmental organizations (Rivanna Water and Sewer Authority, Thomas Jefferson Planning District Commission).