The San Luis Rey River supports some of the most extensive riparian habitat in southern California. Largely un-channelized and relatively undisturbed by the massive flood-control alterations suffered by other streams in the region, the San Luis Rey, like the Santa Margarita River just to the north, appears to be of major importance to riparian bird species in the region. The habitat quality generally improves upstream, and may be divided into a lower stretch (Bonsall east to I-15) and an upper stretch (Pala east to Lake Henshaw) that includes the communities of Pauma Valley and Rincon Springs. Major tributaries with significant riparian vegetation along the upper stretch include Pilgrim Creek. While the upper stretch is located largely within public lands (U.S. Forest Service), the lower stretch is owned by numerous small landowners, making large conservation efforts here more challenging. Lake Henshaw, a large, shallow reservoir fed by the San Luis Rey River in northeastern San Diego County, lies in a broad, grassy valley within the Peninsular Range. The surrounding grassland is one of the most extensive in southern California, which is rimmed by ancient oak woodland (incl. the largest expanse of Engelmann Oak Woodland in the world) and scattered conifers. There is very little public access in the area, as it is mainly private ranchland and Indian Reservation.
The upper stretch of the San Luis Rey River, particularly the 4-mi. stretch below Lake Henshaw, is one of three main nesting areas for Southwestern Willow Flycatcher in California. This represents a significant proportion of the global population of this taxon. Least Bell's Vireo breeds in abundance, with nearly 200 pairs along the upper San Luis Rey River and Pilgrim Creek. Guajome Lake, located at the western end of the IBA, is a haven for breeding freshwater marsh birds, such as Snowy Egret, Least Bittern and Marsh Wren, as well as San Diego County's only nesting colony of White-faced Ibis, one of only a handful in southern California (San Diego History Museum of Natural History 2002). The lower stretch still supports a vibrant riparian bird community, and one of great local importance in this rapidly-developing area (Oceanside-Vista). Large numbers of Least Bell's Vireo breed here, along with a handful of Long-eared Owl (one of the few remaining coastal locations in southern California). The Lake Henshaw area is notable both for its grassland and alkali flat bird community, which includes nesting species such as Grasshopper Sparrow and an exceptional diversity and number of wintering raptors (including Ferruginous Hawk, Prairie Falcon, and Burrowing, Long-eared and Short-eared owls), which seem concentrated in the grassland east of the lake (known as hawk alley by local birders). Lake Henshaw appears to be a regionally-important wintering locale for Bald Eagle and American White Pelican. Due to its position along the major spring migration corridor between the Colorado Desert and the coastal slope of California, the Lake Henshaw area sees a large movement of long-distance migrants such as Swainson's Hawk, which often land in the grassland to rest during migration, as well as many species of waterfowl and shorebirds, whose numbers are imperfectly known due to the difficulty of access.
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Efforts to stem urban encroachment of the lower San Luis Rey River will continue to be important as the region builds out. The area is located in the heart of San Diego County's Indian casino country, and there are many proposals to site new gaming facilities and associated development such as hotel construction and road-widening/stream channelization (fide K. Weaver). The expansion and creation of new sand-mining operations have posed a serious threat to riparian birds for years. Associated disturbances (e.g. Brown-headed Cowbirds) are probably a major threat to breeding songbirds, at least on the lower San Luis Rey. Since cowbird parasitism appears to not be a major threat to the bird community along the upper San Luis Rey, the principal disturbance here is from recreation. As the key riparian areas happen to coincide with established campgrounds, large numbers of people may be found swimming or rafting (in inner tubes) on the river on summer weekends, and, locally, trampling the riparian vegetation. The impact of these activities should be assessed. Also, irregular water discharge from Lake Henshaw may be adversely affecting habitat values in both stretches and should be studied.
While the upper stretch is located largely within public lands (U.S. Forest Service), the lower stretch is owned by numerous small landowners.
The San Luis Rey River watershed supports some of the most extensive riparian habitat in southern California. Major tributaries with significant riparian vegetation along the upper stretch include Pilgrim Creek.