Key Issues

The SLR River in the Southern Subbasin is not hydrologically connected to flows in the Middle and Upper subbasins; therefore, the majority river is dry from late spring until the occurrence of significant rains in the fall or winter;

Numerous unregulated wells throughout the subbasin most likely have a negative impact on stream flows in the SLR River and some of its tributaries;

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;

Multiple partial barriers are located in the SLR River within the subbasin, hindering the potential upstream movement of steelhead and any potential emigration of juvenile trout down into the estuary and eventually into the ocean;

Non-native plants, such as Arundo donax occupy large areas along the SLR River and in a couple of its tributaries, particularly in the western portion of the subbasin;

Agricultural wastewater runoff poses a potential problem to aquatic ecosystems in the SLR River and its tributaries.

Findings Related to Issues

Flow and Water Quality:

The SLR River in the Southern Subbasin is not hydrologically connected to flows in the Middle and Upper subbasins as the river water is diverted to the Escondido Canal. Water flows are also seriously impacted by numerous extraction pumps and other anthropogenic uses located throughout the subbasin;

The lack of flows or sufficient flows in the SLR River most likely would impede the passage of steelhead to more suitable tributaries located in the Northern Subbasin and potential habitat in the SLR River canyon;

Water quality is being impacted by agricultural runoff that have direct access to streams.

Erosion/Sediment:

Without significant, channel altering flows, the movement of bedload materials in the SLR River is severely limited;

The river’s lack of hydrologic connectivity with the Middle and Upper subbasins also most likely hinders potential gravel recruitment;

Removal of native vegetation for crop production has increased the amount of fine sediments entering tributaries and the SLR River during or after rain events;

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

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

Riparian Condition/Water Temperature:

Canopy cover is not suitable for salmonids. The SLR River has wide stream banks with generally sparse canopy. What canopy is available over streams is composed mostly of shrubs and grassland vegetation;

The vegetation communities along the river have been significantly altered due to the severely diminished surface flows and conversion to agriculture. Riparian vegetation once consisting of willows, cottonwoods, oaks and other typical southern California riparian tree and shrub species have largely been replaced with agricultural crops, mixed sagebrush/chaparral and herbaceous vegetation communities;

Invasive, exotic plant species, specifically Arundo, is widespread in the western portion of the subbasin in the mainstem and along some of the tributaries;/li>

Water temperature data collected by CDFG during summer habitat inventories are limited, and therefore inconclusive.

Instream Habitat:

Due to the lack of sufficient surface flows, moderate to high quality salmonid habitat is lacking in the majority of the SLR River within the subbasin. The river is mostly devoid of riparian vegetation, contains high sediment levels, lacks potential spawning gravels, and displays minimum instream habitat diversity;

The exception being is in the SLR River canyon where perennial flows coupled with cool water temperatures and deep pools provide a considerable amount of suitable O. mykiss habitat;

The one tributary that was surveyed, Keys Creek, did not contain suitable steelhead/trout habitat below a natural bedrock chute barrier at RM 2.2. The first half mile of the creek contained a concrete-lined channel, which gave way to dense stands of giant reed that dominated the left and right banks.

Gravel/Substrate:

Suitable salmonid spawning areas were very limited in surveyed reaches of the SLR River and Keys Creek. 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 few potential spawning gravels are a result of the natural channel morphology, lack of hydrologic connectivity from the middle and upper watershed, which prevents gravel recruitment, and past and present human related activities.

Refugia Areas:

A NMFS biologist who surveyed a portion of the mainstem within the SLR River canyon in the summer of 2009 concluded that the habitat below the waterfall (RM 39.5) within the inner gorge could serve as over summering refugia habitat for O. mykiss (M. Capelli, personal communication 2009);

Salmonid habitat conditions in the CDFG surveyed portions of Keys Creek are generally rated as low potential refugia;

Current habitat status is relatively unknown for a few other tributaries, such as Hells Creek and Paradise Creek, but no historical records exist of steelhead/trout utilization of these streams. Considering the majority of these streams’ reaches are labeled as intermittent streams on USGS 7.5 quadrangles, it seems unlikely that they would contain even moderate quality habitat.

Barriers:

The Escondido Canal diversion dam (RM 40) is a complete barrier and the natural waterfall in the SLR River canyon at “Kye” (RM 39.5) is most likely impassible due to the altered flow regime. Both of these barriers are located along the SLR River in the eastern portion of the subbasin;

Partial barriers that would significantly hinder the passage of steelhead/trout in the SLR River include Arizona Road crossing at Cole Grade Road and two road crossings in the Pauma Valley Country Club Golf Course;

Several other roads crossing exist on the SLR River containing either culverts or concrete-lined channel bottoms with significant gradient changes, which create seasonal/temporary fish passage problems;

Keys Creek contains a natural boulder chute approximately 2.2 miles upstream its confluence with the SLR River and appeared to be impassible to steelhead/trout;

Moosa Canyon also has a small, man-made dam approximately 1 mile upstream from its confluence with the SLR River that trout are unlikely to successfully pass.