Birding Site Guide: San Elijo Lagoon

San Elijo Lagoon, California. High tide: From N Rios Ave looking north
across the lagoon to the Nature Center on the other side.

San Elijo Lagoon is probably my favorite birding locale in San Diego County. It could be because it was one of the first places I ever birded in San Diego County. Local birder Terry Hunefeld showed me around in 2008. It has waterbirds of all descriptions and some trails through coastal sage scrub. Two specialty species can be found--Clapper Rail and California Gnatcatcher. It is good for finding a variety of birds in good numbers at close range for photography. Rare birds I've discovered here include Nelson's Sparrow and Prothonotary Warbler. There are several access points, but here I discuss two.

South side: N Rios Avenue, Solana Beach
Getting there: Solana Beach is 25 miles north of downtown San Diego on Interstate 5. Exit I-5 at Lomas Santa Fe Dr and follow it west almost 1 mile. Turn right (north) on N Rios Ave and take it 1 mile to the end. Parking: There is free street parking here. Hours: Dawn to dusk. Map navigation: 899 N Rios Ave, Solana Beach, CA 92075.

North side: San Elijo Lagoon Nature Center, Encinitas (Cardiff-by-the-Sea)
Getting there: Take I-5 North (as above) and exit 1 mile farther north on Manchester Avenue. Loop around and under I-5 to the west about a mile to the Nature Center. Parking: Free parking lot at the Nature Center. Hours: 9:00 am to 5:00 pm. For earlier arrival, if you drive up over the rounded curb, perhaps 3 cars can park on the shoulder of Manchester Ave near the entrance. Map navigation: San Elijo Lagoon Nature Center, 2710 Manchester Avenue, Encinitas, CA 92007

N Rios Ave

Update: The entire estuary is being modified back to a natural salt marsh. Work is in phases to protect the native wildlife that exists. When completed (estimated to be June 2020) it will be possible to hike around the entire wetland in a big loop. That may be about 4 miles, but will certainly be worth it! It means that until then, from Rios Avenue, only the trail from A to D is open. Trails to B and C are closed.

Where to bird: From the street parking at the end of N Rios Ave ("A" on the map above) there are two ways to go. You probably want to bird both ways, but which one first depends upon you. This is a popular place for joggers and dog walkers. Perhaps you want to bird near the water first, before foot traffic moves water birds out away from the edges.

The trail down the hill to the west has a spur out into the marsh ("B" (dead center on top photo)). This is a favorite location for Belding's Savannah Sparrows and Marsh Wrens. This is where I discovered a Nelson's Sparrow during an extreme high tide on January 1, 2014.

The trail continues below the residential area (Allen's Hummingbirds on the hillside) where there are cattails and duck ponds. Listen for Sora and Clapper Rails here. After the pump station the trail parallels a ditch below the commuter rail tracks and out past some pond scrapes ("C"). These scrapes are excellent for shorebirds when they have water. The edge of the marsh here is also good for larger shorebirds and herons, depending upon tidal stage. You can walk farther, if birds are present. Otherwise these ponds ("C") are a good place to turn back. Be sure to check the winter sparrow flocks here.

Back at the parking area ("A") again you may wish to shed your early morning jacket and rehydrate for the next portion. There is great birding at the parking area on the bluff overlooking the lagoon. The residential area will have Hooded Orioles spring through fall. There are many trees below the parking area that usually has good bird activity.

N Rios Ave trailhead looking east toward I-5.

Following the trail east it first heads through some deciduous riparian "woods" below the residential area. Then the trail leads out into the coastal sage-scrub habitat. About a half mile from the parking lot is a little side canyon leading up to some eucalyptus trees ("D"). The lower portion of the canyon is your best bet for California Gnatcatcher (Blue-gray Gnatcatchers are in the sage loop nearer the water). The scattered trees here will host Nuttall's Woodpeckers and Cassin's Kingbirds. I don't often go much farther than this, but there is a more extensive eucalyptus grove nearer I-5 that might be good for Neo-tropical migrants in spring or fall.

South side of Lagoon looking toward the ocean. The N Rios Rd
trailhead is left of the houses 1/2 mile distant.

San Elijo Lagoon Nature Center

Where to bird: From the Nature Center parking lot ("E" on map above) walk the loop trails. I'd walk the entire perimeter, then cut through the middle and back to the nature center walking on the marsh side again--about 1 mile total.

The trail through the willow tangles and woods should be really good for migrant birds, but I have yet to really hit a fallout here. American Goldfinches and Downy Woodpeckers reach the southern edge of their range here. Sometimes you get a closer view of some waterbirds. Frankly, if you bird N Rios Ave, you can probably safely skip this portion. Probably. But I think the habitat here has the potential for some really good finds--better than what I've found so far. Although I did find Prothonotary Warbler at the entrance one morning in late October.

The Nature Center trail leads through a small grove of endangered Torrey Pines.

Marlene and Cosette ("Cosi") come along for a walk on the Nature Center trail.

eBird Hotspot bar charts:
San Elijo Lagoon--Nature Center Loop  175 species
San Elijo Lagoon--Rios Ave entrance  189 species
San Elijo Lagoon--west (combined above areas and beach)  222 species