Study Area

Surveys for the Southwestern Willow Flycatcher were completed in 2025 at five locations in San Diego County: one along the San Dieguito River near Escondido and four along the upper San Luis Rey River near Santa Ysabel (fig. 1). The San Dieguito River survey location (San Dieguito [SD]) consisted of an approximately 10.5-kilometer (km) reach of the San Dieguito River upstream from Interstate 15 (I–15; fig. 1) that was last surveyed in 2016 (Howell and others, 2022). The survey area included property owned by the City of San Diego Public Utilities Department.

Riparian habitat at San Dieguito included a mix of mature willow (Salix spp.), Fremont cottonwood (Populus fremontii), and non-native tamarisk (Tamarix ramosissima), with some mule fat (Baccharis salicifolia) present. Understory vegetation included native vegetation, such as poison oak (Toxicodendron diversilobum) and stinging nettle (Urtica dioica), interspersed with non-native giant reed (Arundo donax), poison hemlock (Conium maculatum), artichoke thistle (Cynara cardunculus), perennial pepperweed (Lepidium latifolium), and black mustard (Brassica nigra).

The upper San Luis Rey River survey area consisted of an approximately 6.9-km reach of the San Luis Rey River downstream from Lake Henshaw and the habitat surrounding Lake Henshaw (fig. 1). Four locations along the upper San Luis Rey River were surveyed for flycatchers in 2025, including three locations downstream from the Henshaw dam that have been surveyed annually since 2015 (Rey River Ranch [RRR], Cleveland National Forest [CNF], and Vista Irrigation District [VID]) and one location upstream from the Henshaw dam that has been surveyed annually since 2018 (VID Lake Henshaw [VLH]). The survey area included property managed by VID, CNF, and private property downstream from the Forest Service property. Surface flows were regulated by a dam at Lake Henshaw operated by VID, and water was present year-round. In most years, spring and summer flows were swift, and slow-moving backwater/marshy habitats were absent. In 2025, however, there was very little water in the San Luis Rey River, and some sections were completely dry. The flood plain in the downstream part of the study area was narrow and bordered by steep slopes that supported chaparral vegetation. Riparian habitat downstream included a diverse mix of mature willow (Salix spp.) and coast live oak (Quercus agrifolia) woodlands, dominated by coast live oak, willow, velvet ash (Fraxinus velutina), California sycamore (Platanus racemosa), and white alder (Alnus rhombifolia).

Thick understory vegetation was present, including California wildrose (Rosa californica), poison oak, stinging nettle, and California blackberry (Rubus ursinus), interspersed with patches of open habitat dominated by annual grasses and bracken fern (Pteridium sp.). The habitat surrounding Lake Henshaw was dominated by Goodding’s black willow (Salix gooddingii), with some arroyo willow (Salix lasiolepis), red willow (Salix laevigata), Fremont cottonwood, and coast live oak where the west fork of the San Luis Rey River and several other minor creeks flowed into the lake. There were several patches of non-native tamarisk present. In 2023, above-average precipitation (114.5 centimeters [cm], 172 percent of mean from 1960 to 2022 [66.7 cm]; J. Sherwood, Vista Irrigation District, written commun., 2024) resulted in a lake level that partially inundated flycatcher habitat at Lake Henshaw. All understory vegetation was submerged, but the tops of mature willow, cottonwood, and tamarisk trees extended above the water line in some sections. Although the lake level lowered in 2024 after a year of average precipitation (67.2 cm; J. Sherwood, Vista Irrigation District, written commun., 2024), most of the flycatcher habitat continued to be submerged, and evidence of tree death was prominent. This habitat decline was especially apparent among cottonwood and tamarisk trees; most specimens of these two species were not leafed out and appeared to be dead. Black willow, a dominant tree species at Lake Henshaw, was affected at the high water line, and many trees snapped and fell over; however, some vertical shoots emerged from the horizontal trunks, indicating that the trees were still alive. At the beginning of the 2025 survey season (May), the trunks and roots of most trees in the areas historically occupied by flycatchers still were submerged in water from 0.5–1 m deep, which slowly receded over the course of the breeding season. In 2025, most cottonwood and tamarisk trees that had been submerged since February 2023 were dead, but most of the black willows survived more than 2 years of inundation.

Surveys

U.S. Geological Survey biologists Lisa Allen, Scarlett Howell, Suellen Lynn, and Shannon Mendia completed flycatcher surveys following a standardized call back survey protocol for Southwestern Willow Flycatchers (Sogge and others, 2010). The survey protocol is designed to increase the likelihood of detecting Southwestern Willow Flycatchers and aid in determining their breeding status by performing repeated surveys during the early to mid-nesting season, with three to four surveys carried out at least 5 days apart during three consecutive survey periods between May 15 and July 31. One survey was done between May 15 and May 31, one survey between June 1 and June 24, and one to two surveys between June 25 and July 31. Survey areas found to have breeding flycatchers received a second survey in the June 25 to July 31 period to increase the likelihood of detecting fledglings. Surveys were done between dawn and early afternoon, avoiding periods of inclement weather, such as temperatures below freezing, rain, or strong winds that inhibit detection of flycatchers. In areas accessible by foot, surveys were done by walking next to the river or lake, using caution to avoid disturbing the habitat or damaging nests. In wider stands, observers traversed the habitat, choosing routes that permitted detection of all birds throughout its extent, such as multiple straight transects, serpentine, zig-zag, or crisscross routes. In flooded habitat, surveys were done by boat, primarily by moving along the outside edge of the habitat patch and entering the interior habitat whenever possible. By mid-July, most flycatcher habitat could be reached on foot; however, large numbers of downed trees in 2025 prevented surveyors from accessing the interior habitat in some sections that could not be reached on foot, which may have resulted in an underestimate of the number of flycatcher territories present in these areas.

Upon initiation of the survey, investigators stood quietly for 1–2 minutes, listening for spontaneously singing flycatchers and acclimating to surrounding conditions, such as road and river noise. During boat surveys, investigators stopped the boat engine and floated quietly during the listening period. If there were no birds detected during the initial listening period, investigators broadcasted flycatcher song (“fitz-bew”) using an MP3 player or mobile phone and an amplified speaker at the volume of typical bird songs for approximately 10–15 seconds and then looked and listened for approximately 1 minute for a response. Flycatchers typically responded by moving silently toward the song, singing in response to the song, or by producing some other call or vocalization. Song playback was ceased immediately upon detection of a flycatcher. Additional flycatcher vocalizations were broadcast occasionally during boat-based surveys to elicit a response and confirm flycatcher presence. This procedure was repeated (including a 10-second quiet pre-broadcast listening period) every 20–30 m throughout land-based survey sites or 80–100 m throughout boat-based survey sites and more frequently if background noise was loud. If a flycatcher was detected, the investigator moved approximately 50–80 m beyond the detection before additional playback occurred to avoid double counting birds. At most flycatcher territories, flycatchers in adjacent territories could be heard vocalizing simultaneously.

For each flycatcher encountered, observers recorded age (adult or juvenile), sex (male, female, or unknown), breeding status (paired, undetermined, or transient), and whenever possible, if the bird was banded. Flycatcher age was determined by the physical appearance of plumage (for example, juveniles [fledged young-of-the-year] exhibited buffy wing bars) combined with behavioral cues, such as territorial defense or singing. Sex determination was based on behavioral observations of adult flycatchers detected during each survey visit. For example, males often broadcast song continuously from conspicuous perches, whereas females sing only occasionally (Seutin, 1987; Sedgwick and Knopf, 1989). Females perform most of the nest building and incubation (U.S. Fish and Wildlife Service, 2002). If we could not confidently assign a sex during surveys, the flycatcher’s sex was recorded as unknown. Breeding status of adult flycatchers was based on the culmination of behavioral observations observed over multiple visits. Flycatchers were considered paired if (1) a second flycatcher was present and unchallenged by the territorial male during more than one survey period, (2) male/female interactions were observed, (3) an adult flycatcher was observed carrying nesting material or food, (4) an active flycatcher nest was located, or (5) adults were observed actively feeding fledglings. To avoid overcounting male flycatchers, observers attempted to determine pairing type (monogamous or polygynous). Monogamous pairings consisted of one male paired with one female, whereas polygynous pairings consisted of one male paired with more than one female. Behaviors used to establish polygyny included males interacting with more than one female simultaneously or sequentially. For example, during a territory visit, observers often documented a male/female interaction in territory A while simultaneously hearing a third flycatcher vocalizing (for example, whitting) in the adjacent territory B, and when the territory A interaction ended, a male/female interaction was subsequently heard in territory B while the female in territory A simultaneously began vocalizing. Flycatcher breeding status was considered undetermined when behaviors, such as spontaneous singing or other territory defense, were observed during the non-migration period (from approximately June 15 to July 20; Sogge and others, 2010), but no pair behaviors were confirmed. A flycatcher was considered transient if detected only once, or if twice, was detected over two successive survey periods in which detections were less than 2 weeks apart.

Adult flycatcher locations were mapped using Environmental Systems Research Institute Field Maps (Esri, 2025) on mobile phones with built-in Global Positioning System to determine geographic coordinates (World Geodetic System 1984). Habitat was characterized by visual inspection within 50 m of each flycatcher location. Dominant native and exotic plants were recorded at each location, and percent cover of native vegetation was estimated using cover categories of less than 5 percent, 5–50 percent, 51–95 percent, and greater than 95 percent. Overall habitat type was specified according to the following categories:

Nest Monitoring

From May 15 to August 22, U.S. Geological Survey biologists Scarlett Howell and Suellen Lynn monitored nesting attempts of paired flycatchers at Lake Henshaw to determine nest success, productivity, and cowbird parasitism rate (percentage of nests parasitized). Pairs were observed for evidence of nesting, and when vegetation structure allowed access, their nests were located and monitored following standard protocol (Rourke and others, 1999). To minimize the chances of leading predators or cowbirds to nest sites, nests were visited only as frequently as needed to collect sufficient data, and nests were not approached when predators or cowbirds were present (Rourke and others, 1999). Typically, there were three to four visits per nest, corresponding to about one visit per week. The first visits were timed to determine the number of eggs (cowbird and flycatcher) laid; subsequent visits were to determine hatching status and the age of any young, and the final visit was to confirm fledging. Whenever possible, cowbird eggs were removed from parasitized nests and destroyed to promote nest success because parasitized flycatcher nests are rarely successful in fledging host young (Rothstein and others, 2003). As flycatchers readily renest after failure, biologists frequently located and monitored more than one nest in a flycatcher territory. Field surveys and nest monitoring were authorized by U.S. Fish and Wildlife Service10(a)1(A) Recovery Permit ESPER0004080_0.3 and were approved by the U.S. Geological Survey Western Ecological Research Center Animal Care and Use Committee.

Nests were assigned six possible fates based on the following parameters. Nests that fledged at least one young were considered successful (SUC). Fledging was confirmed by detection of young outside the nest. Unsuccessful nests were placed into one of five nest fate categories. Nests found empty or destroyed prior to the estimated fledge date were considered depredated (PRE), as were nests where the adult flycatchers were not found tending fledgling(s). Previously active nests that were subsequently abandoned by adult flycatchers after one or more cowbird eggs were laid in the nest were considered to have failed because of nest parasitism (PAR). Any nests that fledged cowbird young without fledging flycatcher young also were considered to have failed because of nest parasitism (PAR). Nests failing for reasons such as poor nest construction, the collapse of a host plant that caused a nest’s contents to be dumped onto the ground, or the presence of an unhatched clutch of eggs that were presumed to be infertile, were classified as failing because of other causes that were known (OTH). Nests that appeared intact and undisturbed but were abandoned with flycatcher eggs before the earliest hatch date or nests that were completed but failed before flycatcher eggs could be confirmed were classified as having failed because of unknown causes (UNK). Nests that were found empty and intact after the estimated fledge date, but no fledgling(s) could be confirmed, and no adults were detected in the territory, were also classified as UNK. Finally, nests that were seen during the construction phase but never completed or that showed evidence of being dismantled before flycatcher eggs were confirmed in the nest were classified as “incomplete” (INC).

We used information collected during territory and nest visits to determine nest initiation dates (date first egg laid), apparent nest success (the proportion of completed nests that fledged young), productivity (the number of young fledged per pair), and fledge date (the date on which fledging occurred, estimated from the nest chronology) or fail date (the date that a nest was discovered failed, or backward-dated based on the timing of a renest). We used the presence of cowbird eggs in flycatcher nests to calculate the percentage of nests parasitized, based on nests in which the contents were observed.

Banded Bird Resighting

Flycatchers were banded at three locations (RRR, CNF, and VID) as part of a separate demographic study from 2015 to 2019 (Howell and others, 2022). In that study, adults were captured at monitored territories using mist nets and song playback and were banded with a unique color-band combination. Nestlings from accessible nests were banded with a single metal dark blue band on the left or right leg. In subsequent years, flycatchers that were resighted with a single dark blue band (“natal”) were recaptured and given a second leg band to yield a unique color-band combination. In 2025, we attempted to resight all flycatchers to identify individuals based on color-band combinations. If banded birds were detected, color-band resighting data were used to determine age and document movement from banding sites.

Abundance and Distribution

In 2025, there were 57 territorial flycatchers and 3 transient flycatchers of unknown subspecies observed during surveys. All flycatchers were detected along the upper San Luis Rey River at VLH (figs. 2, 3; tables 1, 2). No flycatchers were detected at any of the survey locations downstream from Lake Henshaw or at San Dieguito. The flycatcher population at VLH increased 21 percent from 2024 (47 territorial flycatchers; Howell and Kus, 2022b, 2025) to 2025 (Howell and Kus, 2022b). There were 37 territories established at VLH, containing 35 pairs (20 males and 35 females) and 2 male flycatchers of undetermined breeding status. Of the 35 pairs, 12 were monogamous pairings, and 23 were polygynous pairings consisting of 3 males each pairing with 2 different females [6 pairs], 3 males each pairing with 3 different females [9 pairs], and 2 males each pairing with 4 different females [8 pairs]).

The distribution of flycatcher territories along the upper San Luis Rey River has shifted since 2018 when Lake Henshaw was first surveyed. From 2018 to 2023, the combined population of flycatchers downstream from Lake Henshaw (CNF, RRR, VID) decreased annually before falling to zero territories in 2023, whereas the population upstream from Henshaw dam (VLH) increased from 2018 to 2021, declined slightly in 2022, increased in 2023, declined significantly in 2024, and increased in 2025 (fig. 3).

In 2025, all flycatcher detections were in mixed willow habitat type, dominated exclusively by Goodding’s black willow. Exotic vegetation was not prevalent in the survey area; 93 percent (37/40) of flycatcher locations occurred in habitat with greater than 95-percent native plant cover. Most of the exotic vegetation consisted of non-native annuals, such as sweet clover (Melilotus spp.).

Nest Monitoring

Of the 35 territories at VLH that contained paired flycatchers, 26 were monitored during the 2025 breeding season. There were 40 flycatcher nests located and monitored, and of these, 7 were incomplete (table 3). Of the 33 completed nests, 30 percent (10) successfully fledged young. Two additional nests in two separate territories were not located but were successful based on the presence of fledglings. Of the 23 failed nests, 61 percent were depredated (14), 22 percent failed for unknown reasons (5), and 17 percent failed because of cowbird parasitism (4). There were 33 fledglings confirmed, yielding a seasonal productivity of 1.3 young/pair (33 young/26 monitored pairs). One additional fledgling was confirmed in an unmonitored territory during surveys at VLH (table 2).

Brown-headed Cowbirds

Cowbirds were detected at all five survey locations. During nest monitoring activities, we were able to observe the contents of 31 flycatcher nests. Seven of these nests (23 percent) were parasitized, each containing one cowbird egg (table 3). In 2025, all nests that contained a cowbird egg were too high to access the nest contents, and no cowbird eggs were removed. Of the seven parasitized nests, only one nest was ultimately successful after the cowbird egg failed to hatch (MLH01F nest 4; table 3). In two additional territories, adult flycatchers were observed feeding a cowbird fledgling.

Banded Birds

No banded flycatchers present in previous years were observed in 2025. However, flooded conditions made entering the interior habitat difficult, and we were unable to access the exact territory locations where banded birds were last observed in 2022.