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Rainbow Creek Watershed

Rainbow Creek begins east of Rainbow Valley and flows west through the Valley, then under old Highway 395 and the Interstate-15 Freeway. West of the freeway, the creek flows through the northern portion of Fallbrook before converging with the Santa Margarita River. Rainbow Creek Watershed lies within the larger Santa Margarita Watershed and encompasses 7,085 acres, mostly in San Diego County with a small portion in Riverside County. Land use in the watershed is primarily rural, undeveloped land. Several agricultural operations, including orchards, groves, commercial nurseries, and mixed use fields are within Rainbow Creek Watershed. Visit Living in a Healthy Watershed to learn about how residents and visitors in the Rainbow Creek Watershed can have a positive impact on the watershed and humans, plants and animals that live, play and work in it.


The terrain of Rainbow Creek Watershed is mostly hilly with some steep slopes and a flat valley floor. The watershed’s elevation ranges from 2,070 feet above sea level in the eastern portion, to just 400 feet above sea level at the base of the watershed in the western portion. Rainbow Valley has an elevation of approximately 1,100 to 1,050 feet above sea level.

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Large quantities of water are imported into Rainbow Valley, mainly for agricultural irrigation, but also for residential and limited commercial use. The geology and shape of Rainbow Valley allow for high rates of water infiltration from this imported water. The unconfined groundwater aquifer below Rainbow Valley has a high water table, meaning that water can be found at relatively shallow depths below the soil’s surface in many portions of Rainbow Valley. The water table may be higher in some areas due to agricultural irrigation and residential or commercial septic system leach fields. In addition to high groundwater levels, imported water has resulted in increased flows in Rainbow Creek, with some portions having flow year round.

The high groundwater levels in Rainbow Valley increase the potential for groundwater pollution. Shallow soils drastically reduce the potential for water filtration before it reaches the groundwater basin. Nitrogen and phosphorus from agricultural runoff and nitrogen from septic systems significantly contribute to groundwater pollution in Rainbow Valley. Nitrogen and phosphorus, among other contaminants, have led to the degradation of ground water and surface water quality in Rainbow Creek. The San Diego Regional Water Quality Control Board has adopted Total Maximum Daily Loads (TMDLs) for Total Nitrogen and Total Phosphorus to address the water quality impairments in Rainbow Creek. The Rainbow Municipal Water District has published the Rainbow Valley Basin Groundwater Management Plan in an effort to manage the ground water for potential potable use.

In order to reduce water pollution in the Rainbow Creek Watershed, in the 1970s the County of San Diego placed a ban on the installation of new or replacement septic tank disposal systems in areas of Rainbow Valley with a high ground water levels. This ban was implemented as septic systems could not be installed in compliance with the requirements at the time due to the high ground water table. Existing septic systems in the Rainbow Creek Watershed have leach fields that are close to or submerged in the groundwater during all or part of the year. Proper septic system maintenance is critical to keeping the water within Rainbow Creek Watershed healthy.