Key Issues

Water quantity has been greatly reduced as water resources have been over allocated. The hydrologic connectivity of the SLR River Basin has been significantly altered due to dams, water diversions, and extensive pumping of the underground aquifers throughout the basin;

Water quality is impaired in some tributaries and in the lower SLR River;

Accessibility to potential spawning and rearing habitat is blocked at various points in the basin;

Introduction of exotic flora and fauna have adversely altered riparian communities and habitat conditions along the SLR River and some of its tributaries;

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

Historic and current land use has altered watershed processes and conditions;

Alterations to watershed processes have affected the basin both socially and economically;

Overall loss of estuarine habitat and estuarine function has been adversely affected;

Fish and wildlife have been adversely impacted by current watershed conditions in the basin.

Findings Related to Issues

Flow and Water Quality:

Intermittent and perennial flows exist in areas with potentially suitable habitat: SLR River within the SLR River canyon (approximately RM 37 to the natural waterfall barrier, RM 39.5) as well as portions of the Northern Subbasin tributaries, such as Pauma Creek, Aqua Tibia Creek, Frey Creek, Gomez Creek, and Pala Creek;

The Southern and Coastal subbasins are not hydrologically connected to flows in the Middle and Upper subbasins. Flows have been altered throughout the basin as Henshaw Dam impedes flows into the Middle Subbasin and then downstream as Escondido Canal diversion diverts virtually all flows out of the mainstem at the upper end of the Southern Subbasin;

Dry or intermittent reaches on the SLR mainstem prevent connection with the estuary and thus the ocean and hinders the recovery of steelhead in the basin;

Stream flows in tributaries have been reduced or in some cases eliminated through extraction for anthropogenic use;

Perennial stream flows in the SLR River exist in most of the Middle Subbasin from just downstream of Henshaw Dam to the Escondido Canal diversion, in the SLR River canyon (RM 37-39.5), and in several locations in the Coast Subbasin, such as the area around Interstate 15 downstream to the town of Bonsall and near the Ocean. Many tributaries throughout the watershed also possess sections of perennial stream flows;

The SLR River is listed as impaired by the SDRWQCB for Total Dissolved Solids, chloride and fecal coliform (at the mouth);

Water quality is most likely being impacted in the Upper Subbasin by cattle defecating near Lake Henshaw or in streams flowing into Lake Henshaw;

According to the 2003-2005 Ambient Bay and Lagoon Monitoring Program, the benthic community health in the SLR River estuary was assessed as “poor to fair.” The program rated toxicology and chemistry as “good” for two out of the three years of monitoring (Weston Solutions 2007).


Due to the natural occurring geology within the majority of the basin, which consisting of loosely consolidated sediments, bank erosion and land sliding along the streams is present;

Natural and human related sedimentation within the watershed has resulted in an overall loss of spawning, rearing and feeding habitat for salmonids within the basin;

The dominant material below Pala (Southern Subbasin) is median sand, which is highly transportable during floods, limiting spawning and rearing habitat in the Coastal and lower portions of the Southern subbasins;

Henshaw Dam and the Escondido Canal diversion dam reduce the transport of sediments that would normally help to replenish beach sand along the coast and various substrates in the riverbed;

Although soil erosion from crops have been minimized through Best Management Practices, due to the large scale farming and roads associated with these operations soil erosion is expected to still occur within the basin. This erosion has degraded aquatic habitat;

The 2007 wildfires, which occurred in large areas of the Northern and Southern subbasins, caused debris flows and increased runoff and erosion, resulting in higher than usual peak flows along stream channels. Ash and other sediment/nutrient loads has washed and blown into ephemeral and perennial streams.

Riparian Condition/Water Temperature:

U.S. Army Corps of Engineers planned vegetation removal (Operation and Maintenance Plan) for flood control purposes will greatly alter the riparian structure in the Coastal Subbasin resulting in serious impacts to the aquatic habitat. These impacts are as follows: loss of overstory shade, reduction in necessary cover from predation, decreasing components that contribute to pool formation, lessening of macro-invertebrate production, and decline in bank stabilization;

While the Operation and Maintenance Plan in the Coastal Subbasin will adversely remove a great deal of native riparian willow and cottonwood trees, it will however, help to eradicate areas that have become overgrown with giant reed, Arundo donax, which has numerous negative impacts on the riparian and stream habitat;

The Coastal Subbasin had suitable canopy density measurements, but a good percentage of these canopy measurements were aided by the dense stands of Arundo that lined the stream channel or occupied the stream channel itself. The lowest reach in the Coastal Subbasin had a poor canopy rating, but this was attributed to the wide river channel, limiting the extent of the overstory canopy;

The majority (70%) of the mainstem reaches surveyed in the Middle Subbasin and tributary reaches within the Northern Subbasin met or nearly met the target value of 80% canopy coverage with the exception of the uppermost reach in the SLR River in the Middle Subbasin. Canopy cover in these reaches was composed of mature forest canopy consisting of alders and oaks and to a lesser extent cottonwoods and willow;

The majority of the surveyed SLR River in the Southern Subbasin, however, is largely devoid of tree bankside vegetation except for areas in the western portion of the subbasin and isolated patches elsewhere. Most of the riparian vegetation was composed of shrubs and grassland species;

Water temperatures recorded during the 2007 CDFG surveys of streams in the SLR River Basin indicate ‘unsuitable to moderately unsuitable’ temperatures for salmonids in the Coastal Subbasin and ‘suitable’ in the Middle and Northern subbasins; however, these water temperature data are limited, and therefore inconclusive;

Hobo thermometers were placed in various locations in the SLR River and in a few tributaries, Gomez Creek and Moosa Canyon Creek, during the temperature extreme period (spring through fall for 2008 & 2009). Overall, the 2008 recorded data displayed unsuitable water temperatures in the estuary during the summer months; however, water temperatures in the tributaries and middle SLR River were considered suitable throughout data collection period;

Stream temperatures could increase in the Coastal Subbasin with the removal of riparian canopy due to the Flood Control Project.

Instream Habitat:

Quality pool structure is generally lacking in the mainstem throughout the basin. All surveyed reaches had an inadequate number of pools and the overall length of pool habitat was lacking; while a few of the reaches contained adequate shelter, only one reach surveyed met standards for preferred pool depths;

Pauma Creek contained the most suitable instream habitat conditions of the tributary and SLR River reaches evaluated during the assessment; however, some tributaries and sections of the SLR River could not be surveyed due to denied access. Subsequently, a NMFS biologist performed a general reconnaissance survey of the mainstem within the SLR River canyon in the summer of 2009 and described the area as having suitable over summering refugia habitat based on perennial stream flows with cool water temperatures and a few deep pools with boulder cover;

Stream bioassessments were performed (independently of CDFG’s habitat surveys) in the lower mainstem SLR River and a reference site on a tributary of Pauma Creek and provide an indication of overall stream health. The SLR River urban sites had Index of Biotic Integrity Ratings of Very Poor during both surveys, while the Doane Creek reference site was the highest rated site in the county program, with the greatest taxonomic diversity (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 and Relative Benthic Index scores.


Due to the geology of basin and increased sedimentation from anthropogenic practices, the SLR River streambed has been described as silted in 2007 CDFG stream habitat inventories;

Less than 5% of pool tail outs in the SLR River have cobble embeddedness in categories one and two, which meet spawning gravel targets for salmonids. The SLR River and its tributaries in the Coastal and Southern subbasins (downstream of the SLR River canyon) offer very little potential spawning habitat;

Surveyed reaches in the SLR River upstream of the Escondido Canal diversion dam contain pockets of potential spawning gravels, but overall suitable spawning areas are also limited;

Henshaw Dam and the Escondido Canal diversion dam severely limits the recruitment of new gravel and cobble from the middle and upper watershed, which is needed downstream for spawning habitat and overall habitat diversity in the SLR River;

Areas containing suitable spawning gravels exist throughout Pauma Creek and were observed in portions of Gomez Creek. Other tributaries in the Northern Subbasin, such as Agua Tibia Creek, Frey Creek, and Pala Creek most likely contain suitable substrate for spawning as well.

Refugia Areas:

The Northern Subbasin (Pauma Creek) provides medium potential refugia. Additional refugia areas may be present in several other Northern Subbasin tributaries, including Gomez Creek, Agua Tibia Creek, Frey Creek, and Pala Creek. However, a majority of the refugia in this subbasin is inaccessible to steelhead due to lack of river flows, multiple barriers throughout Coastal and Southern subbasins, and additional barriers in the Northern Subbasin tributaries;

While most of the Southern Subbasin is devoid of surface flows for the majority of the year and is uninhabitable for fish, the upper portion of the subbasin within the SLR River canyon (RM 37-39.5) contains perennial flowing water with pool habitats, instream cover, and most likely suitable water temperatures due to the rising groundwater and small tributaries and springs. This stretch of river could serve as spawning and over summering refugia habitat;

The Coastal Subbasin provide lower quality refugia. The subbasin could provide critical instream and estuarine rearing habitat if riparian areas were maintained and habitat restoration projects were implemented in the mainstem and estuary;

The Middle Subbasin is inaccessible to ocean run fish due to the Escondido Canal diversion dam at RM 40 and further hindered by the altered flow regime and additional fish passage problems downstream. Overall, the Middle Subbasin provides low quality refugia;

Some suitable trout habitat exists in the streams of the Upper Subbasin as evident by the self-sustaining native rainbow trout populations in the WF SLR River and should be maintained as resident, native fish habitat.


Numerous partial and complete barriers exist on the mainstem of the SLR River and its tributaries that do not meet CDFG and NOAA Fisheries fish passage guidelines. In the Coastal Subbasin, three partial barriers are located along the SLR River that prevent passage to certain life stages of steelhead at certain times of the year;

The SLR River in the Southern Subbasin contains a complete barrier in the Escondido Canal diversion dam at RM 40. A natural waterfall barrier at RM 39.5 would prevent fish passage during most flow conditions. Four partial barriers (such as Cole Grade Road crossing on the SLR River and road crossing in the Pauma Valley Country Club) and two additional barriers whose passage status are unknown exists below the natural waterfall barrier;

Tributaries in the Northern Subbasin that have fish passage barriers include Pauma Creek, Gomez Creek, Frey Creek, Agua Tibia Creek, and Pala Creek, which limit steelhead access to potentially significant refugia areas;

The Middle Subbasin contains two complete barriers: a natural bedrock chute/waterfall approximately two miles downstream of Henshaw Dam and Henshaw Dam itself. Several non-structural, partial barriers were also observed within the middle to upper survey area.

Key Recommendations

Flow and Water Quality Improvement Activities:

Further analysis is needed to determine if water releases, seasonally appropriate pulse flows, through Henshaw Dam and the Escondido Canal diversion dam could ameliorate the adverse conditions affecting steelhead recovery in the SLR River and how much water would be required to provide minimum stream flows necessary for steelhead adult and juvenile migration in the SLR River;

These flushing flows would also allow natural hydrologic processes to occur, which are important to creating and developing instream habitat, improve riverine restoration, restoring hydrologic processes and provide sediment delivery for much needed beach sand replacement; however, longstanding water rights and water settlements, such as the Settlement Act, would limit opportunities to provide water for restoration/recovery activities;

Enforce maximum irrigation efficiency with both agricultural and urban users. Implement the reuse of treated gray water for irrigation purposes;

Strongly encourage homeowners to reduce their overall water use by converting lawns and landscaping to drought tolerant, native plants;

Continue to build upon current region wide water conservation programs that are being enforced in many cities and municipals;

Work with private property owners to establish conservation easements in the watershed, particularly along or near riverine habitats;

Maximize fertilizer and pesticide efficiency and utilize integrated pest management to reduce overall use of pesticides.

Barrier Modification Activities:

Modify existing fish passage barriers at public and private road crossings and other man-made barriers along the SLR River. Modification of partial barriers in the SLR River within the Coastal and lower Southern subbasins, such as the boulder rip-rap configuration under Douglas Avenue bridge and would be relatively low-cost projects that would facilitate the migration of both adult and juvenile fish during all flow conditions;

Further fish passage barrier modifications in Northern Subbasin streams, such as Pauma, Agua Tibia, Frey, and Gomez creeks are necessary for steelhead to access potential suitable spawning and rearing habitats. While some of these barrier modifications may be more costly, they are essential for the successful completion of their freshwater lifecycle stages.

Erosion and Sediment Delivery Reduction Activities:

The impact of property subdivision on streams of the SLR Basin should be minimized through the use of better land management practices and stormwater pollution prevention programs;

Continue to encourage the use of Best Management Practices (BMPs) for nutrient runoff, pesticide management, and erosion control for homeowners and agricultural and industrial uses. The Natural Resource Conservation Services, local Resource Conservation District, and the Farm and Home Advisors’ Office have been integral in the information and assistance in these practices;

Existing sediment production problem sites that have potential to deliver sediments to streams should be evaluated and mitigated.

Riparian and Habitat Improvement Activities:

Develop and implement a restoration and management plan for the SLR River estuary. This includes identifying and prioritizing locations within the estuary where vegetation can be returned to salt tolerant species, thus improving the habitat recovery of the estuary for all marine dependent species that may use the estuary;

Control and management of Arundo and other invasive plant species within the SLR River watershed requires a coordinated, watershed-wide approach. Ongoing efforts to remove Arundo should focus on upper populations in the watershed to prevent reinfestation of treated downstream sites from upstream sources. Continuous monitoring and eradication efforts must be performed in order to prevent the re-colonization of exotics and allow for the establishment of natives;

Support the Mission RCD in its efforts to eradicate and remove exotic plant species in the Coastal and Southern subbasins;

Release of water from dams in seasonal appropriate flood pulses may enhance establishment of riparian species such as cottonwood and willow in cohorts that may survive for decades. This would be especially important along the SLR River in the Southern Subbasin;

Programs to increase riparian vegetation should be implemented in streams where shade canopy is below target values of 80% coverage. This was evident along the SLR River in the Southern Subbasin. Any riparian planting must take into consideration the presence of invasive plant species and the hydrologic processes of the river in order to make a sustained, beneficial impact;

Replace annual grasses with native perennial grasses. This would help the regeneration of oak savanna habitat and potentially improve groundwater storage in portions of the basin;

In creeks where fish spawning and rearing habitat is limited, pool enhancement and instream structures should be added to increase complexity. Due to the lack of potential spawning gravels throughout the watershed, the placement of cobbles and gravels from outside resources in key locations, where stream flows are sufficient and rearing habitat is present, may improve the probability and success of steelhead spawning in the SLR River Basin;

In order to protect riparian vegetation, and decrease stream bank erosion due to unrestricted access of cattle to streams, use of livestock management fencing should be prescribed where necessary.

Education, Research, and Monitoring Activities:

Continue to build upon current educational outreach to the community concerning the elimination of exotic flora and fauna plantings and stockings;

Expand education programs in schools and community outreach to promote water conservation in the watershed;

Implement or expand on educational programs in schools and communities about the issue of fire, its benefits, drawbacks, and prevention;

Research private property available for purchase by public agencies and non-profit groups, for various habitat conservation and open space plans;

Conduct stream habitat and fish inventories in the SLR River canyon and in streams of the Northern Subbasin, including Gomez, Aqua Tibia, Frey, and Pala Creeks;

Partner with local academic institutions and private agencies as a means to encourage the study of fish and habitat;

Explore the potential of installing a steelhead counting station downstream of Bonsall as a means of establishing abundance and trends of adult anadromous runs of steelhead and juvenile migration;

Continue to monitor summer/early fall water temperatures in the estuary, lower SLR River, and important tributaries in the Northern Subbasin for at least a three to five year period;

Consider an economic study to determine the cost of water needed for steelhead recovery as well as its impact on the local stakeholders;

Continue to monitor the potential effects of new and existing wells in the Coastal Subbasin concerning reduced surface flows and/or a lowered groundwater table, thus effecting wetlands and riparian areas and enabling saltwater intrusion;

In the estuary, the completion of the Pacific Street bridge replacement will partially restore the natural flow regime. Water quality and estuary conditions will require monitoring. Salinities should be collected in the estuary and upstream to determine the extent of brackish conditions. Biological surveys should be performed in the estuary for at least a three year period;

Continue to monitor the potential effects of the 2007 fires on sediment input, habitat and fish populations in the Pauma Creek watershed and the SLR River.