The broad challenges faced by steelhead emigrating through the SR–SJR Delta are representative of those faced by salmonids in estuaries of other river systems. The combination of habitat loss, reduced river flows, increased resource use, warming temperatures, and non-native aquatic community structure is intensified in the SJR Delta by its southern latitude in the steelhead range and by human development of the region. Other populations are soon likely to face comparable challenges as a result of climate change, growing population density, and expanded modification of estuary habitat (Magnusson and Hilborn 2003
; Moyle et al. 2008
). Studies of both Pacific salmonids and Atlantic salmon (Salmo salar
) demonstrate that survival of juvenile salmonids tends to be lower and more variable in estuaries than in either river or marine habitats (Welch et al. 2011
; Thorstad et al. 2012
). Thus, understanding estuarine survival is of paramount importance to population persistence. This study was the first to yield a multi-year time series of spatially detailed steelhead estuarine survival estimates and has demonstrated that survival varies considerably spatially, between years, and seasonally through this inland estuary. This level of variability would not have been apparent from a study shorter in duration. Despite the effort required to estimate estuarine survival, multi-year time series are necessary to represent the variability in conditions and survival experienced by steelhead populations in these environments.
This study presents the first direct estimates of survival of CV steelhead as they emigrate from the SJR through the SR–SJR Delta. The few previous CV steelhead survival studies focused on steelhead emigrating from the SR, representing the northern components of the CV Evolutionarily Significant Unit, and presented results from only single study years or for only broad spatial areas (Singer et al. 2013
; Brodsky et al. 2020
; Sandstrom et al. 2020
). Historically, management approaches for SJR steelhead have been geared toward Chinook salmon rather than steelhead patterns of migration and habitat use, and steelhead survival has been inferred from adult escapement and CWT data from salmon (McEwan 2001
). These acoustic-telemetry estimates show that steelhead survival through the Delta varies considerably both between and within years: release-level survival estimates from Mossdale to Chipps Island varied from 0.06 to 0.69 (Table 4
). These survival levels are more variable and often considerably higher than those observed for fall-run Chinook Salmon migrating through the same regions at similar times, which were consistently ≤0.05 for 2011–2014 (Buchanan et al. 2015
). However, these steelhead survival estimates were comparable to or lower than those reported for SR steelhead and late fall-run Chinook salmon migrating through the Delta from the north only a few months earlier in mid- to late-winter (Singer et al. 2013
; Perry et al. 2013
; Michel et al. 2015
; Sandstrom et al. 2020
). The temporal and spatial variation in survival across the CV demonstrates the continuing need for acoustic telemetry studies using relevant populations of juvenile salmonids to understand potential ecological processes and management strategies linked to survival, rather than inferring these measures from past studies or different basins.
Although monitoring the performance of imperiled populations is preferred for their management, studying such populations is often difficult. Regulations and small population sizes may prevent collection of individuals from protected species and individuals suitable for tagging may represent only larger size classes or late juvenile life stages. In this study, we used yearling hatchery fish from MRFH to represent steelhead emigrating from the SJR basin. Although MRFH steelhead are included in the threatened CV DPS and this hatchery is in the SJR basin, the SJR steelhead that emigrate past our release site are naturally produced rather than hatchery fish. Differences have been found in survival patterns between wild and hatchery salmonids in the Columbia River basin and may exist between the hatchery and wild components of the CV DPS as well (Buchanan et al. 2010
; Murphy et al. 2011
). Nevertheless, we believe that hatchery steelhead provide better inference than hatchery Chinook Salmon, which have otherwise been the basis for management of SJR steelhead. Other considerations include tag size, which may limit the individuals available for study, and tag effects on survival performance. This study used multiple strategies to limit or eliminate tag effects, and we recommend the same for future studies. Additionally, increased monitoring of juvenile steelhead exiting upstream tributaries would facilitate characterization of the proportion of run-of-river emigrants represented by the tagged fish.
Management strategies designed to support steelhead survival in the Delta have included keeping fish out of the OR route, releasing water from upstream reservoirs to increase river inflow to the Delta, and limiting water pumping rates at the export facilities in the spring when the fish are migrating. The I:E ratio has been used as a regulatory metric to moderate water export rates and Delta inflow. The results in this study provide a look at how consistent actual steelhead survival patterns are with these management strategies and demonstrate agreement with some expected patterns but not others. Estimated survival was higher when the barrier was in place at the head of OR and when Delta inflow and the I:E ratio were higher, as expected. However, survival was not notably higher in the SJR route compared to the OR route or for lower export rates, contrary to expectations. Furthermore, different survival processes were apparent in adjacent habitats, indicating that actions to support survival should also be spatially defined.
The lack of a consistent route-specific survival difference between the SJR and OR routes was surprising, considering that both water export facilities are located in the OR route. Although the point estimates of survival were higher for the SJR route compared to the OR route for 16 of 19 release groups (Table 4
), the differences were sometimes very small and were not statistically significant when adjusted for year, barrier status, and fork length (P
= 0.1282). The barrier affects route selection at the head of OR by blocking most access to the OR route, so it is possible that the perceived barrier effect was at least partially a route effect: if the SJR route is superior and the barrier directs fish into that route, then the barrier effect would be positive. If this were true, then a route effect should be observed whether or not the barrier was present. However, the within-year difference between annual route-specific survival estimates was close to 0 (−0.04 to 0.03) for years without the barrier and ranged up to 0.27 for years when the barrier was installed. Additionally, the barrier effect was significant even when route was accounted for (P
= 0.0207), and AIC was lower for a barrier model over a route model (ΔAIC = 15.3). These results suggest that perceived survival differences between the routes were primarily due to the presence of the temporary rock barrier. The fact that survival was not associated with route further suggests that it was the barrier’s influence on hydrodynamic conditions in the SJR that contributed to higher survival by diverting SJR inflow away from OR and into the lower SJR. Likewise, the survival modeling for the SJR route upstream of the TCJ suggests that survival benefits in this reach can be attained either by increasing Delta inflow or by installing the barrier. The mechanical nature of the barrier’s action, i.e., diversion of both fish and water, lends support to the hypothesis that the perceived survival differences associated with the barrier are due to the barrier’s physical presence rather than to other, unacknowledged variables (e.g., season). Discontinuation of barrier use in future years may have a negative effect on steelhead survival in the Delta unless additional management strategies are implemented to direct both fish and flow into the SJR, such as modifying hydrodynamics or channel morphology in the head of OR region.
This work represented the OR route effect as a difference in total survival probability to Chipps Island in the OR route compared to the SJR route. This is reasonable for identifying factors associated with overall fish fate in this region (successfully leave the Delta vs. mortality in the Delta). An alternative assessment of route effects would explore the relative differences in survival rate per kilometre rather than total survival probability, i.e., σ
for route length d
. Because different routes have different lengths, a route effect on the survival rate scale may not be apparent on the total survival scale. A similar consideration applies to daily survival rate. A difficulty in modeling survival rate rather than total survival probability is identifying a well-defined migration route distance: both the OR and SJR routes from the head of OR include multiple subroutes of varying lengths. In the OR route, the migration pathway from the head of OR to Chipps Island is approximately 45 km via the salvage subroutes (omitting distance trucked) but is 88 km via OR itself (bold line in Fig. 1c
). In the SJR route, the total migration pathway is approximately 88 km via the mainstem SJR compared to up to 100 km via the salvage facilities, depending on routing choices at TCJ and throughout the interior Delta (Fig. 1b
). We performed a preliminary survival rate analysis using an OR route length weighted toward the salvage subroutes (km = 55) and a SJR route length representing non-salvage subroutes (km = 88). Using these route lengths to define survival rate per kilometre, we found a significant negative effect of the OR route on the survival rate (P
< 0.0001), suggesting more intense mortality forces in the OR route. This is consistent with expectations that the OR route is more treacherous but is highly sensitive to the migration route lengths assumed in analysis and appears to have been largely offset by the actual pathway lengths experienced by the study fish in the OR and SJR routes when considering total survival probability to Delta exit. Future work will investigate the migration route distances more fully and the potential effect of routing choices on survival in and through the Delta.
The relationship between SJR inflow and survival was particularly strong and, together with year, barrier status, and fork length, accounted for all the variation in survival that was associated with other environmental and operational covariates. The positive relationship between SJR inflow and survival translated to a positive relationship between the I:E ratio and survival as well. Several mechanisms may contribute to the positive relationship observed between inflow and survival. One possibility is that higher flows result in faster water velocities and shorter travel times, so that fish are at risk of mortality in the study area for a shorter period of time (Anderson et al. 2005
). Travel time was negatively associated with SJR inflow in the tidal transitional reach from the head of OR to the TCJ (P
= 0.0001), where there was also a positive relationship between SJR inflow and survival, consistent with this hypothesis. However, travel time was also negatively associated with SJR inflow in the tidal reach between TCJ and Chipps Island (P
= 0.0363), where survival was unrelated to inflow. This heterogeneous spatial pattern is consistent with findings in Perry et al. (2018)
for the northern Delta. Alternatively, higher flows are associated with lower temperatures, higher levels of dissolved oxygen, and lower levels of contaminants (Sinokrot and Gulliver 2000
; Monsen et al. 2007
; Grossman 2016
), all of which may influence survival. It is likely that more than one mechanism accounts for the inflow-survival relationship observed.
Despite the strong findings for Delta inflow, there were limitations to the dependence of survival on inflow. The first year of the study, 2011, was a high flow year and had daily inflow values that were 1.5 to 91 times the inflow observed in the other five years of the study (Fig. 3
). Nevertheless, some release groups from 2011 had survival estimates that were comparable to or lower than those seen in drier years (Table 4
). The high flow in 2011 prevented installation of the barrier at the head of OR; it appears that the barrier may help mitigate for effects of low flows in drier years (Fig. 7
). Additionally, the inflow-survival relationship was notably absent in the region between the TCJ and Chipps Island. The region downstream (i.e., north and west) of the TCJ is strongly tidally dominated, and it is reasonable that environmental conditions there are largely insensitive to SJR inflow from >50 rkm upstream. Additional management strategies beyond reservoir releases and the head of OR barrier will be needed to improve survival in this region.
Current management strategies assume that survival is lower when Delta exports are higher, in particular because of the increased risk of migration delay at the facilities or entrainment at the pumps. There is also thought to be a large population of predators in and within close proximity to the facilities (Grossman 2016
; Moyle et al. 2017
). Nevertheless, this study found no association between export rate and survival from the head of OR to Chipps Island (P
≥ 0.2228; Table 5
). There was weak support for an association between survival and the CVP proportion of combined exports (pCVP; P
= 0.0196), which measures the allocation of exports across the two large export facilities; even this evidence was inconclusive, however, given the large number of covariates considered. On the other hand, we observed a positive association between export rate and survival in the SJR main stem upstream of the TCJ when the barrier was in place. This was surprising because fish in this reach are not near the export facilities and hydrodynamics models have found little effect of exports on flow and velocity patterns in this region (Cavallo et al. 2013
). However, export rate and Delta inflow tend to be positively correlated (partial correlation coefficient = 0.56, P
< 0.0001, after adjusting for year with the barrier in place) and survival was more strongly associated with SJR inflow than with exports in this reach, so the association between exports and survival in the SJR main stem may result from an inflow effect rather than causal export effects. Overall, we recommend that the export rate results be viewed in the context of existing policy, which uses the I:E ratio regulatory metric to dictate restricted export levels during the spring outmigration and thus low variability in export levels during the tagging study. For example, during the study period each year, mean daily combined (CVP+SWP) export levels were ≤6100 cfs, compared to values up to 12 862 cfs during the full 2011–2016 water years (October to September). The relatively low variability in export levels in this study makes it difficult to detect potential survival effects; it is conceivable that different survival patterns might be exhibited under unrestricted (i.e., higher) exports, especially in the OR route which passes the entrances to the pumping facilities. For these reasons, the assessment of exports reported here should not be interpreted as a complete assessment of the policy that defines allowable export operations in the spring but rather an assessment of the variability in exports actually observed in the springs of 2011–2016.
The survival patterns observed in relation to the barrier and to some extent exports help explain the surprisingly high through-Delta survival observed in the extreme drought year of 2015 (Table 5
). Of the six years in the study, 2015 had the lowest inflow, highest temperatures, and highest X2 (salinity) levels (Fig. 3
). Despite the harsh conditions, the overall estimated probability of survival from Mossdale to Chipps Island in 2015 (0.23) was considerably higher than for 2013 (0.14), which was also a drought year but had higher inflow, slightly lower temperatures, and lower X2. However, export levels were lower and less variable in the 2015 study (mean 1765 cfs) than in the 2013 study (mean = 2464 cfs; Fig. 4
), and the barrier was installed for the majority of 2015 but not in 2013. Average fork length at tagging was also higher in 2015 (235 mm) than in 2013 (212 mm). Survival in the SJR route was considerably higher in 2015 than in 2013, and it was also higher than in the OR route in 2015, consistent with a positive barrier effect. Comparison of these years demonstrates the potentially mitigating effects of fish size, the head of OR barrier, and lower exports in very low flow years. Although these factors are insufficient to fully compensate for lack of water entering the Delta, they may help prevent very low survival that could lead to further declines in anadromous O. mykiss
Despite the lack of route-specific survival differences from the head of OR to Chipps Island, there was a strong survival difference between the mainstem (SJR) route and the interior Delta (TC) route from the TCJ (P
< 0.0001). Remaining in the SJR route at TCJ was estimated to increase the survival probability to Chipps Island by up to 0.44 (Fig. 9
). This finding is similar to observations that late-fall-run Chinook salmon and steelhead migrating from the SR had lower survival in interior Delta routes than in mainstem river routes (Perry et al. 2010
; Singer et al. 2013
). The interior Delta connects the mainstem river to the water export facilities located in the SW Delta, and one hypothesis is that entering the interior Delta at the TCJ lowers survival by increasing the risk of entrainment at the facilities; entrained fish that are salvaged may appear at Chipps Island as successful Delta migrants, but those that are not salvaged are lost to the pumps, water conveyance canals, or predation and appear as mortalities in the statistical models. Indeed, of the 489 steelhead detected entering TC, 135 (28%) were subsequently detected at the water export facility entrances, compared to 5% of the 1451 fish using the SJR mainstem route from the TCJ. However, the route with the highest proportion of fish entering the facilities was the OR route: 67% of the fish in that route, compared to only 8% of the fish that chose the SJR route at the head of OR. If increased entrainment was the source of the reduced survival in the TC route, then we would also expect to see markedly lower survival in the OR route compared to the SJR route from the head of OR. This was not observed. Another possibility is that the habitat in the interior Delta results in higher mortality risk compared to the mainstem river. The TC route leads fish to the central portion of the interior Delta, which is also the region encountered by SR salmon that enter the interior Delta. This region includes several submerged islands that have low water velocities, low turbidity, dense mats of non-native vegetation such as Brazilian waterweed (Egeria densa
), and populations of non-native, warm-water predatory fish such as largemouth bass (Nobriga and Feyrer 2007
; Conrad et al. 2016
). Although the late-fall-run Chinook salmon from the SR studies migrate through the region in winter when predation rates are expected to be lower compared to this study’s spring steelhead migration, the lake-type habitat common in the central region of the interior Delta may pose similar challenges to both populations of migrating salmonids. Preventing fish from entering the interior Delta at TC is challenging because the hydrodynamics in the junction do not allow for a barrier to be installed, and fish may enter the interior Delta through multiple routes from further downstream. Instead, management strategies to improve habitat in the interior Delta for native fish and make it less desirable for non-native predators may have the potential to increase survival in this region for salmonids migrating from both the SJR basin and the SR basin.
Precipitation patterns in California are projected to be more volatile under climate change, with more frequent and extreme droughts and also more extreme flood events (Dettinger 2011
; Diffenbaugh et al. 2015
; Swain et al. 2018
), and one question managers face is how mitigation strategies may be affected by drought. This study showed evidence of a drought effect on steelhead survival through the Delta, in particular in the OR route and in the SJR downstream to the TCJ; survival through these regions tended to be higher in non-drought years. However, investigation efforts were hampered by the large differences in flow among the non-drought years, in particular between 2011 (wet year) and the dry years of 2012 and 2016. Although both drought status and water year status varied by year, neither criterion fully accounted for the year effects in the survival models. This result hinders efforts to predict survival as a function of drought status without better understanding of the factors that drive year effects.
Drought may affect survival patterns in the Delta in several ways, including lowering inflows and increasing temperatures. One mechanism by which drought may affect survival is to move the location of the zone where the habitat transitions from unidirectional flow to bidirectional tidal flows. This transition zone and its dependence on Delta inflow may be critical to the relationship between inflow and survival (Perry et al. 2018
). A shift of that transition zone farther upstream during drought would introduce migrating salmonids to reverse flows and altered water quality factors earlier in their migration. In the SJR, the transition reach lies between the head of OR and the TCJ most years, depending on inflow conditions and barrier status at the head of OR (Cavallo et al. 2013
; National Oceanic and Atmospheric Administration Fisheries Salmon Scoping Team 2017
). Because the barrier keeps more river flow in the SJR, it is expected to keep the location of the transition farther downstream even in drought years, and thus may be an important mitigating factor for low inflow during drought. These possibilities are supported by cumulative survival curves from this study, which show that for all three drought years and only one non-drought year, the SJR reach that had the highest mortality rate downstream of the head of OR was in the upstream portion of the stretch from OR to the TCJ, specifically from OR to Garwood Bridge (SJG; Fig. 6
). The mortality rate to Garwood Bridge was noticeably higher in the drought years than in the wet and dry years and was the highest in 2013, the only drought year without a barrier installed at the head of OR (Fig. 6
). Efforts to mitigate effects of drought should include improving habitat for migrating salmonids in this reach as well as either installing the barrier at the head of OR or redesigning channel morphology at that river junction to keep more flow in the SJR. These actions may be especially important to support steelhead populations as climate change affects the frequency of drought and lower seasonal flows.
This study is a step forward in understanding the temporal and spatial variability in survival of CV steelhead populations as they emigrate through the San Joaquin Delta and the factors that affect survival. Although the specific results are unique to this population, a similar degree of spatial and temporal variability may be expected in other estuarine systems. Likewise, the investigative and analytical approaches used in this paper may be employed in other systems to monitor steelhead performance through the crucial estuarine juvenile life stage and inform management strategies to support the anadromous life history. The results here have implications for management designed to support emigrant survival in the Delta, including timing reservoir releases from the multiple SJR tributaries to coincide with the juvenile migration, directing more flow down the SJR rather than OR, and restoring habitat south of TC and in the central interior Delta. There is more work to be done in studying this threatened population, and future tagging studies will provide data for testing the models developed here. Questions for future investigation include the factors driving route selection at various junctions in the Delta, juvenile steelhead residence time and the propensity of Delta rearing, reach-specific flow–survival relationships, survival differences between hatchery and run-of-river steelhead and between steelhead and Chinook salmon, the role of non-native predators and non-native vegetation on survival patterns in different regions of the Delta, and the sensitivity of adult returns to estuarine and early marine survival. Another important management need is estimating steelhead survival further downstream through the bays. Understanding these and other issues will be necessary to support the anadromous component of the CV’s O. mykiss population and maintain the life history diversity necessary for this population to persist in a changing climate.