Key Issues

The Coastal Subbasin is not hydrologically connected to flows in the Middle and Upper subbasins, which adversely impacts water quality and quantity, complex instream habitat, native flora and fauna, recruitment of new streambed substrates and providing beach sand replacement along the coast;

Invasive plant species, Arundo and Tamarisk, have altered the riparian landscape and degraded instream habitat conditions of the SLR River;

The natural function of the SLR River estuary, which once sprawled more than 2,200 acres, has been altered considerably by the marina, urban development, and on-going flood protection activities within the estuary and floodplain area. Presently, the estuary has been downsized to an approximately 164 acre floodplain with degraded habitat conditions;

Urban and agricultural runoff poses a problem to aquatic ecosystems in the mainstem SLR River;

Partial fish passage barriers exist throughout the SLR River within the subbasin;

Sediment level in streams is high and creates a multitude of problems for fish habitat;

The river’s streambed is most likely still negatively impacted by previous upstream gravel mining practices.

Findings Related to Issues

Flow and Water Quality:

The Coastal Subbasin is not hydrologically connected to flows in the Middle and Upper subbasins as practically all river flows are diverted to the Escondido Canal. Stream flows are also seriously impacted by numerous extraction pumps and other anthropogenic uses located throughout the subbasin;

Low summer flows may be stressful to salmonids, and dry or intermittent reaches on the SLR River seasonally prevent connection to the estuary;

Water quality is being impacted by agricultural and urban runoff that have direct access to streams;

The SLR River urban sites had an Index of Biotic Ratings of Very Poor during both surveys. The in-stream physical habitat of these sites was qualified as marginal, which could have limited macroinvertebrate colonization. Erosion/Sediment:

Excessive sediment in stream channels has resulted in an overall loss of spawning, rearing and feeding habitat for salmonids. The majority of the SLR River channel is composed of Quaternary Alluvium consisting of sand and silt. High sediment levels are confirmed by embeddedness measurements in surveyed reaches;

Livestock have unrestricted access to some tributaries, resulting in stream bank erosion;

Soils (and bedrock) in streams of the Coastal Subbasin are prone to erosion, and slides and streambank failures have been observed to contribute fines to the streams.

Riparian Condition/Water Temperature:

Canopy density measurements on the SLR obtained suitable values on three of the four reaches. The lower reach, where canopy target values were not met are partially related to the naturally, broad river channel. Riparian trees are present, but are not tall enough to sufficiently cover the entire river;

Invasive plant species such as Arundo donax and Tamarisk sp. are widespread and have displaced large amount of native riparian vegetation;

The Corps Operation and Maintenance Plan in the lower seven miles of the river channel has removed and will continue to remove large amounts of vegetation over the next couple of years. This will adversely affect the canopy cover in this area;

Water temperature data collected by CDFG during summer habitat inventories indicate acceptable levels, with some streams nearing stressful conditions. However, these data are limited, and therefore inconclusive.

Instream Habitat:

Based on observations and data recorded during instream habitat inventories, high quality salmonid habitat is lacking in all surveyed reaches of the SLR River within the Coastal Subbasin. Conditions present at the time of the survey indicated a low number of pools as well as a poor percentage of pool habitat by surveyed stream length. Furthermore, the majority of the pools present were shallow and pool shelter cover is generally lacking;

Stream bioassessments performed in the lower mainstem SLR River had Index of Biotic Integrity Ratings of Very Poor during 2005 and 2006 surveys (Weston Solutions 2007);

The SLR estuary’s health assessed during the 2003-2005 period was rated as poor to fair based on analysis of Benthic Response Index (BRI) and Relative Benthic Index (RBI) scores;

Tributaries appear to offer very limited additional spawning and rearing habitat due to low flows and unsuitable instream conditions.


Suitable salmonid spawning areas were limited in surveyed reaches of the SLR River. Overall numbers of potential spawning gravels were low and embeddedness measurements did not meet target values, confirming that sediment levels in the subbasin are high;

The unsuitable embeddedness ratings are the result of the following factors: the natural channel morphology of the alluvial streambed, past (mining) and present human-related activities and the lack of hydrologic connectivity from the middle and upper watershed.

Refugia Areas:

Salmonid habitat conditions on the mainstem are generally rated as low quality refugia;

A few tributaries that were surveyed, but not inventoried, such as Gopher Canyon, Ostrich Creek, and Live Oak Creek, also appeared to provide low quality refugia;

The once expansive SLR River estuary/lagoon could have once provided excellent habitat for rearing juvenile steelhead before their entrance into the ocean. In its current state, the estuary provides low potential refugia as rearing habitat for juvenile fish is limited.


Several partial fish passage barriers exist in the SLR River, such as the rip-rap below the Douglas Avenue and College Avenue bridges, road crossing at RM 11 and a metal sheet spanning the river at RM 17.5 that would seasonally obstruct the upstream movement of adult steelhead and hinder juvenile emigration to the estuary and thus the ocean;

Pilgrim Creek contains possible fish passage barriers in its lower reaches.