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San Juan Creek is a coastal stream in Orange County and Riverside County in the U.S. state of California. The creek drains 133.9 square miles (347 km2) of rugged and partially developed terrain. Because of its lower level of urbanization than many other Orange County streams, the creek supports a large amount of wildlife. Despite that, of the 300 acres (1.2 km2) of rich wetland found in the San Juan Creek watershed, only 0.3 percent remain.
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Vegetation communities
There are sixteen prominent vegetation zones in the San Juan watershed, which include riparian vegetation, sparse woodlands, coastal sage scrub and chaparral. Riparian vegetation is found along the banks of most free-flowing streams in the watershed with a measurable flow for at least part of the year. These include most of San Juan Creek, upper Trabuco Creek, Cañada Gobernadora, Bell Canyon, and most upper tributaries to San Juan Creek, as well as scattered patches along Oso and El Horno creeks. Woodlands are also more prominent in the upper watershed, and also typically occurs in close proximity to waterways. Coastal sage scrub is found on hillsides generally facing south, while chaparral is found at higher-elevation hillsides and mesas. There are also rock outcroppings, freshwater pools, and exotic plant communities within the San Juan watershed, but those are not included in primary plant communities, in part due to their small number. However, exotic plant species, such as giant reed, castor bean, and tobacco tree, are rapidly spreading and have yet to be eradicated. Giant reed is continually responsible for wiping out vast swathes of wetlands, swamps and riparian patches along the creek, although there remains much space where these habitats once thrived.
Animals
Historically, there were up to twelve invertebrate species, five fish species, twelve amphibian species, thirty-five types of reptiles, one hundred forty-three bird species, and forty-two mammal species. Because of the diverse vegetation communities in the San Juan watershed, it is able to support this wide variety of animals. In aquatic communities in the watershed, some federally listed species known to occur include tidewater goby, fairy shrimp, and California red-legged frog. Federally listed bird species include least Bell's vireo, California gnatcatcher, California least tern, and southwestern willow flycatcher. Other listed animals include Pacific pocket mouse and Quino checkerspot butterfly. As urban development continues to grow in the San Juan watershed, however, most sensitive species are now found only in the foothills and mountains, where less development has occurred. However, agriculture and ranching has continued in the foothills and higher valleys, and that is also causing damage to the sensitive wildlife species that inhabit the San Juan watershed.
Steelhead
The creek was a confirmed habitat for steelhead (Oncorhynchus mykiss irideus) in many historic accounts. From the late 1950s-early 1960s to present, the increasing human population in Orange County has produced continuous non-point-source urban runoff that flow into nearby streams, and San Juan Creek is now among the most polluted, with a bacteria occurrence rate that exceeds state standards by 93 percent. Resultantly, not only has the population of steelhead been completely extirpated, but riparian habitat, especially in the lower 2.7 miles (4.3 km) of the creek and much of Trabuco and Oso Creeks, have been eliminated by channelization, which also is reducing steelhead habitat. However, conditions for steelhead have perhaps significantly improved, for it was reported in 2003 by the California Department of Fish and Game up to three times that the steelhead had been sighted in a large stream pool along Trabuco Creek, immediately downstream of a culvert that channels the creek beneath Interstate 5 before spilling it down twin narrow chutes into the pond. In response to this sighting, the Department of Fish and Game persuaded Caltrans to build a fish ladder to assist fish in traversing the structure, but it has not yet been implemented, for reasons including structural stability and the presence of a natural gas pipeline in the vicinity.