Compared to all other major tributaries of the Chesapeake Bay, the reach of the Rappahannock River between Tappahannock and Port Royal remains the most pristine [the same can be said for the area around Rock Stop on the river].  The waterway supports extensive forested wetlands and pristine shorelines embedded within a predominantly rural landscape. Uplands have a wide range of topographic features that result in a high diversity of habitats within a relatively small area. These areas are used for agriculture, forestry, and a growing ornamental nursery industry. Several large farms and historic plantations remain intact. In recent years, the U.S. Fish and Wildlife Service has made the area a focus for acquisition. Surrounding uplands are composed of rural farmlands that support some of the largest grassland bird populations in the Coastal Plain.

A growing and important portion of the IBA is owned and managed for conservation purposes. In recent years the area has become an acquisition target for both the U.S.  Fish and Wildlife Service and The Nature Conservancy. The relatively new Rappahannock River Valley National Wildlife Refuge has been very successful in protecting strategically important tracts within the area. The Virginia Department of Game and Inland Fisheries manages Lands End  Wildlife Management Area for wintering waterfowl. In addition, many private landowners are progressive in managing their lands for conservation benefit.

This reach of the Rappahannock River supports the only known breeding population of Coastal Plain Swamp Sparrows in Virginia. The status and geographic extent of this population remains unknown. The area supports the densest breeding population of Bald Eagles in Virginia and one of the largest summer and winter eagle concentration areas in eastern North America with migrant eagle populations numbering in the hundreds. The waterway is a significant area for waterfowl during the winter months. Forested wetlands support breeding Neotropical migrants such as the Prothonotary Warbler and Yellow-throated Vireo and large winter roosts of blackbirds including the Rusty Blackbird. Surrounding fallow open lands support one of the largest grassland bird communities within coastal Virginia.

Four primary threats are currently of concern including 1) conversion of open land to residential, 2) expansion of recreational boating access to sensitive portions of the river, 3) contaminants within the fishery used by piscivorous birds, and 4) continued expansion of phragmites into sensitive marsh habitats. The urban centers of Fredericksburg and Tappahannock are expanding and expected to place pressure on the rural lands within this area in the future. Waterfront property is particularly vulnerable to future development. Since many of the species that depend on this area are sensitive to development, further development remains a concern. The reach of the river between Tappahannock and Port Royal supports one of the largest winter and summer concentrations of migrant Bald Eagles in eastern North America. These birds have been shown to be very sensitive to boating activity. Increases in boating activity and the number of boat access points within this stretch of the river will negatively impact migrant eagles. In addition, because of their position at the top of the food web, eagles will always be vulnerable to new contaminants entering the system. Pristine marsh habitats and the sensitive species that depend upon it are being threatened by dispersal of the invasive plant phragmites from the large source population on Hoskins Creek. Expansion of this population could seriously impact the integrity of this system to support marsh bird communities.