Excerpts from the Executive summary of the Napa River Basin Limiting Factors Analysis Final Report

Based on evidence of widespread erosion and concerns regarding adverse impacts to fisheries habitat, the Regional Board listed the Napa River and its tributaries in 1990 as impaired by sediment under Section 303(d) of the federal Clean Water Act.

.the Regional Board and Coastal Conservancy funded a two-year study of stream and riparian habitat conditions in the Napa River watershed. The study, conducted by the University of California in collaboration with Stillwater Sciences, evaluated factors limiting populations of three species of rare or threatened native fish and aquatic wildlife in the Napa River watershed.

Although abundance and distribution of several fish and aquatic wildlife species are thought to be substantially diminished, the Napa River basin continues to support a diverse and almost entirely intact community of sixteen native fish species, including steelhead, fall-run Chinook salmon, Pacific and river lamprey (Lampetra tridentata, L. ayresi), hardhead (Mylopharodon conocephalus), hitch (Lavinia exilicauda), tule perch (Hysterocarpus traski), and Sacramento splittail (Pogonichthys macorlepidotus) (Leidy 1997). Such native fish diversity is unsurpassed in Central Valley and Sierra streams, and matched only in a small number of Bay Area streams,

B. Sediment-related Factors

Turbidity

.we measured turbidity under winter baseflow conditions immediately following four storms in 2001 and one larger storm in 2002, to see if these storms could increase turbidity enough to cause a chronic reduction in steelhead feeding efficiency. During water year 2001, we conducted turbidity monitoring at a total of 24 sites (Figure ES-4); 19 sites were sampled to fully characterize the recessional limb of 4 different storms, and the remaining 5 sites were sampled for fewer storms. Turbidity was re-measured at 22 of the 24 original sites in a limited sampling effort to capture conditions after a larger storm event during water year 2002, which was much wetter than 2001. Our results indicate that feeding opportunities were probably not lost for more than one or two days following even the largest storms (based on the 20 NTU estimate). Therefore, turbidity probably did not pose a significant limitation to feeding by steelhead during the period studied.

Within the narrow time frame of this study, no turbidity effects were found, despite our examination of 17 tributaries and 7 sites on the mainstem Napa River. This suggests that there is not a permanently elevated chronic source of sediment causing deleterious turbidity levels. However, our results reflect conditions during only two water years and may not have captured the effects of episodic or rare phenomena such as periods with higher rates of land conversion or road construction or infrequently occurring natural events, such as landslides or extremely large storms.

Pool Filling

We surveyed pool filling during 2001-2002 at 29 reaches in 18 tributaries to the Napa River (Figure ES-4). Our results indicated a median watershed-wide level of pool filling of only 2 percent and confirmed the initial reconnaissance observations that pool filling was not high in the Napa River watershed: 25 of the 29 reaches had index values of <10 percent (21 were less than 5 percent), probably well within the expected range of natural variability.

Gravel Permeability

Initial observations made during field reconnaissance during summer 2000 suggested that the amount of fine sediments present at potential spawning sites was typically low. Considering the potential importance of spawning gravel quality as a limiting factor, and conditions observed at reconnaissance sites, we tested the hypothesis that gravel permeability was not impaired by fine sediment in Napa River tributaries. We measured permeability at 28 reaches in 17 tributaries during field surveys conducted in 2001-2002 (Figure ES-4). Measured permeability values at 28 potential spawning sites for steelhead in Napa River tributaries were lower than those typically found in steelhead streams considered "good" quality (Taggart 1976, McCuddin 1977): the median predicted mortality index value was 55 percent, with 3 of 28 sites having mortality index values greater than 75 percent and no sites having mortality index values lower than 25 percent.

Permeability measured at three potential Chinook/steelhead spawning sites on the mainstem was comparable to the results for the tributaries, with mortality index values of 33, 54, and 57 percent. We concluded that our original hypothesis, that streambed permeability at potential spawning sites was typically sufficient to support high egg survival, is incorrect, and that fine sediment loading may be a widespread problem in the Napa River basin. Further study is needed to establish the causes of the high fine sediment loading to stream channels. However, existing data on fish distribution and abundance (including snorkel surveys conducted throughout most of the watershed in 2001 by Friends of the Napa River and data we collected during summer 2001 in Dry and Ritchie creeks) indicate that a number of Napa River tributaries appear to be relatively well-seeded with juvenile steelhead. Empirical and theoretical evidence suggests that spawning gravel quality and quantity are rarely the primary factors limiting population levels of species such as steelhead and resident trout because a relatively limited amount of successful spawning is capable of seeding large amounts of rearing habitat (Elliot 1984). However, production of fry is still a general concern because extremely low quantity or quality of spawning gravels may be important contributing factors to salmonid population dynamics. The relative importance of reduced permeability as compared to factors, such as the availability of rearing habitat for juveniles, is discussed in the context of a limiting factors analysis below (Section V).

V. DISCUSSION AND SYNTHESIS OF LIMITING FACTORS

A. Chinook salmon

As a result of all the various alterations to the mainstem and its floodplain, the Napa River currently has an extremely limited potential to support a viable population of Chinook salmon. In particular, the dramatic reduction in spawning gravel quantity and quality, coupled with the current high density of exotic predators in the mainstem and loss of off-channel rearing habitat, appear to be the most important limiting factors currently operating in the system.

B. Steelhead

The alterations to the mainstem have likely affected steelhead in a fashion similar to that described above for Chinook salmon, although the impact on the population should have been proportionately smaller since the mainstem provided only a small portion of the potential steelhead spawning and rearing habitat historically present in the watershed.

Our limiting factors analysis for steelhead has therefore focused primarily on the tributaries.

Tributaries to the Napa River are generally steep, coarse-bedded channels with limited pools, except those formed by obstructions (wood, bedrock) or bends. Under current conditions, fine sediment intrusion into spawning gravels is causing low permeability which likely results in relatively low survivorship of steelhead eggs and larvae. Our analysis, however, indicates that a decline in steelhead population levels cannot be attributed to this factor alone. In addition, because Phase I focused on current conditions, we have not established whether the observed levels of fine sediment in spawning gravels are due to natural or anthropogenic causes. The sources of fine sediment and the explanation for its high levels in spawning gravels will be explored in Phase II.

Other alterations to tributaries include numerous dams and road crossings, which serve as barriers or potential impediments to fish passage, reduction in LWD levels, and the likely reduction in flow caused by surface water diversion, groundwater pumping, and various land use activities.

Summer water temperatures in the tributaries are generally warm enough to potentially stress juvenile steelhead, although they are not high enough to be acutely lethal. We do not know whether human land use activities have contributed to these warm temperatures, but we can hypothesize that riparian vegetation removal or alteration coupled with surface and groundwater extraction have likely increased summer water temperatures above historical reference conditions. Testing of this hypothesis has been proposed for Phase II.

Alluvial fans may have provided spawning habitat (although they may naturally have tended to be dry or intermittent seasonally), which, coupled with estuary or lower mainstem rearing, could have led to high steelhead production under historical conditions. Current conditions do not appear favorable for steelhead spawning in the alluvial fan reaches of tributaries or in the mainstem, and the potential for estuary rearing may have been greatly reduced by disking, dredging, or introduction of exotic predators (although we did not evaluate this during Phase I). Testing of this hypothesis has been proposed for Phase II.

To help synthesize the information collected on steelhead habitat conditions, we conducted a population dynamics modeling exercise based on data collected in Ritchie Creek. The modeling results indicate that, under current conditions, the combination of limited spawning gravel quantity and low gravel permeability may be limiting steelhead production to some degree.

Furthermore, our results indicate that current conditions are near a threshold, such that any substantial decrease in spawning gravel quantity or permeability would likely lead to a decline in steelhead production.

C. California freshwater shrimp

Based on the extensive surveys of the mainstem Napa River conducted during Phase I, potential habitat appears to be relatively common (although an average of only three percent of the mainstem banks provide potential habitat). However, a more quantitative assessment is needed to (1) link freshwater shrimp abundance with habitat quality and quantity, (2) determine the distribution of habitat in the Napa River watershed as a whole, and (3) understand the geomorphic processes responsible for forming and maintaining freshwater shrimp habitat. In particular, the importance of overhanging vegetation should be further explored, particularly to assess impacts of cutting back riparian vegetation to minimize blue-green sharpshooter habitat (the vector for Pierce's disease, which attacks grapevines).

Abstract

We found that pool filling with fine sediment is typically quite low with values less than 10 percent at 25 of 29 sites sampled. We also measured turbidity following storm runoff events and found that turbidity typically dropped to very low levels (less than 20 NTU) within 1-to-2 days to following peak runoff events. Therefore we concluded that pool filling and chronic turbidity do not appear to be significant limiting factors for the analysis species under present-day conditions. In contrast, measured values of permeability at potential spawning sites for steelhead and Chinook salmon were typically quite low as a result of fine sediment deposition in the streambed. Based on examination of data relating permeability to survival of incubating salmon eggs and larvae we predicted that mortality of incubating eggs and larvae in Napa River and its tributaries may often exceed 50 % between spawning and emergence. To help evaluate the effect of this level of mortality during incubation on steelhead run size, we performed a quantitative population dynamics modeling exercise using data from one tributary: Ritchie Creek. Based on this analysis, we concluded that current permeability values, although low, might only depress steelhead population by a small amount because it appears that available juvenile rearing habitat can be well seeded even with only 50 % survival during incubation. Our analysis also indicates however, that further reductions in permeability or spawning gravel quantity might cause a substantial decline in steelhead smolt production. Taking these findings into account, the Regional Board has concluded that the Clean Water Act sediment listing should be maintained. Additional studies are needed to determine whether the fine sediments causing low permeability are from natural or anthropogenic sources.

Channel incision and simplification appears to be the primary factor limiting salmon population. Considering the spatial extent, nature, and magnitude of the changes in channel form, we hypothesize that little increase in salmon population would occur as a result of a substantial reduction in total and/or fine bed material supply to the mainstem channel.