Chinook Response to Estuary Restoration

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NOAA NW Fisheries Science Center led a coalition effort to study River Delta Restoration on Salmon populations between 20## and 20##. This involved coordination and integration of River Delta Restoration Monitoring in the Nooksack Delta, Skagit Delta, Stillaguamish Delta, Snohomish Delta, and Nisqually Delta. This work is an expansion of work initiated in Evaluating Salmon Rearing Limitations in River Deltas and leverages hypotheses developed through the Intensively Monitored Watersheds efforts initiated in the Skagit. This effort aims to organize and build on lines of evidence about how change in natal rearing opportunity affects population.

Background

Habitat restoration has been a primary focus of salmon recovery efforts even before many stocks were listed as Threatened or Endangered under the Endangered Species Act. Tidal deltas of major rivers have been a focal habitat to support recovery for threatened Puget Sound Chinook salmon (Oncorhynchus tshawytscha) because of severe losses in these natal estuaries and increased understanding of their importance to juvenile life stages (Healey 1982, Simenstad et al. 1982, Collins et al. 2003, Beamer et al. 2005, Greene et al. 2021). However, while these efforts have undoubtedly created local benefits (Ellings et al. 2016, Greene et al. 2016) and verify that “if you build it, they will come,” their success as part of the recovery framework/toolbox is less understood. In fact, there remains very limited information about how restoration in natal tidal deltas is improving productivity of our Chinook salmon populations. Therefore, this report seeks to address the degree to which capital investments in tidal delta restoration have been successful in terms of realized benefits to Chinook salmon populations, and specifically upon improved growth and survival through juvenile life stages to adult returns.

Methods

To provide an empirical foundation to link individual restoration with population productivity, we tested six primary hypotheses concerning tidal delta wetlands, their restoration, and juvenile Chinook salmon (Fig. 1):

  1. Watershed-specific benefits of tidal delta restoration will depend upon juvenile life history variation.
  2. Estuary restoration projects result in net gain in vegetated tidal wetland habitats
  3. Areas subject to restoration are used by juvenile salmon.
  4. Increasing tidal wetland habitat area (capacity) through restoration will have a positive effect on growth, and mean size and/or condition by extension.
  5. Increasing tidal wetland habitat area produces a positive effect on juvenile survival from freshwater to nearshore marine habitats.
  6. Increasing tidal wetland area has a net positive effect on smolt-adult return rates (SARs)

The first two chapters of this document focus on restoration responses of juvenile Chinook salmon in the Skagit River tidal delta, the location of a wealth of data through the Skagit Intensively Monitored Watershed Project. In Chapter 1, we examined how multiple estuary restoration projects in the Skagit delta affected cohorts of juvenile Chinook salmon, and we found demographic changes consistent with restoration increasing nursery habitat capacity and quality. We took advantage of three decades of surveillance monitoring of juveniles before, during, and after delta restoration; in restored and unrestored forks of the tidal delta; and in locations landward, within, and seaward of the delta. We found that tidal delta restoration was the major source of changes to prime rearing habitat (wetted channels where salmon reside in the delta) since the first project in 2000, although natural changes including significant habitat loss have also occurred (Fig. 2). Areas in the tidal delta generally increased in fish density at higher migrations, yet restored areas in the delta declined in density (Fig. 3A). Body sizes of sampled individuals were smaller at larger migration sizes, and following delta restoration, sampled individuals were smaller overall and their lengths declined less when conspecific densities were higher (Fig. 3B). These findings suggest that greater nursery habitat capacity in the delta attracted smaller individuals and allowed them to both spread out and to accommodate higher juvenile salmon densities when outmigrations were especially high.

Figure 1 (Chapter 4, Fig. 1). Conceptual diagram of how habitat restoration in tidal deltas is predicted to influence habitat conditions and demographic processes affecting the population. Numbers indicate primary hypotheses tested in this report. The core idea is that habitat restoration of the channel network and vegetated wetlands in tidal deltas improves habitat conditions (capacity, connectivity, and opportunity), which in turn benefit the salmon population within the delta and at subsequent stages through carryover effects. Habitat conditions in freshwater and nearshore waters can also affect salmon populations, although they are not the focus of this study. Solid arrows depict relatively instantaneous (within-season or year) effects, while dashed lines represent lagged (multi-year) effects. Double-ended arrows represent two-way effects. Elements addressed in this report are shown in black, while other relevant (unexamined) elements and effects are shown in gray and are italicized.

We also monitored juvenile salmon in nearshore waters seaward of the delta. Catches in nearshore waters, particularly those of migrant fry (<= 45 mm length), increased as a function of in-river migrant abundance pre-restoration (Fig. 3C). Following delta restoration, juvenile catches in nearshore marine waters declined relative to outmigration abundances, and the prevalence of fry in the nearshore decreased (Figure 3D). These results suggest that greater habitat capacity in the tidal delta supported more juveniles, decreasing density-dependent spillover to nearshore environments, especially for the smallest, most vulnerable salmon that presumably benefit most from growth before entering nearshore waters. Thus, estuary restoration

Figure 2 (Chapter 2, Fig. 3). Trends of prime rearing habitat (ha) in four subregions (North Fork (NF), South Fork (SF), Bayfront (BF), and Swinomish Channel (SC)) of the Skagit River delta (left panel), as shown in the map in the right panel using the same color scheme.


Figure 3 (Chapter 1, Figs. 4-7 model predictions). Prediction of benefits of habitat increases, based on modeled relationships of data compiled in the Skagit Intensively Monitored Watershed study.

appeared to alleviate density-dependent constraints on rearing and growth. These findings provide empirical support for restoring estuaries in human-stressed landscapes to rehabilitate nursery habitat functions for salmon and, potentially, other species and life stages.

Because the long-term monitoring results in Chapter 1 uncovered several non-intuitive results based on analysis of cohorts, we sought a second method for evaluating restoration benefits through use of an individual-based model. Such models are ideal for evaluating dynamics of target species that are small, numerous, and highly mobile, thereby greatly complicating standard mark-recapture techniques or other monitoring techniques. This is the case with juvenile salmon using tidal delta habitats – thousands to millions of fish enter at relatively small sizes and can move to and exit the delta via many different channels in the channel network.

In Chapter 2, we explored the use of an individual-based model to ‘track” the behavior, growth, and survival of juvenile Chinook salmon in the Skagit tidal delta as residence and movement is simulated over several scenarios modeling outmigration abundance and extent of restoration. We modeled three naturally observed outmigration abundance scenarios (low, average, and high number of total outmigrants in a year), and restoration scenarios or maps equivalent to 1) pre-restoration, 2) post-restoration of one major project, and 3) further post-restoration of seven additional restoration projects as well as a major natural habitat change (a channel avulsion) in the delta. Restoration scenarios were input as maps of over 10,000 habitat nodes of varying size and connected by pathways determined by blind and distributary channels. Restoration projects resulted in additional nodes and/or pathways. Simulated juvenile migrants entered the delta as fry (<= 45 mm) or parr (> 45 mm), following the observed pattern in outmigration years, and made choices by optimizing the ratio of expected growth to mortality risk, both of which were density- and size- dependent. Simulations ran from February 1 for 165 days. Patterns of residence, distribution, and size change were similar to data from long-term monitoring (see Chapter 1). We found that despite density-dependent growth, restoration improved growth rates for both fry (Fig. 4) and parr entering the delta, and increased overall survival (Fig. 5). These findings help improve understanding of some counterintuitive findings from the Skagit long-term monitoring, as well as show that even moderate restoration can have significant population effects.

Figure 4 (Chapter 2, Fig. 9). Average parr growth rate (log-transformed) by restoration map (columns) and total outmigration scenarios in the two forks of the Skagit delta (colors). Horizontal line denotes threshold below which average growth was negative.


Figure 5 (Chapter 2, Fig. 11).Total survival of all fish by restoration map (columns), and total outmigration size (lines, with thickness tracking annual outmigration population size).

Chapters 1 and 2 focused on restoration responses in one of Puget Sound’s tidal deltas, but these efforts are proceeding across Puget Sound and similarly warrant evaluation at the population level to determine the extent to which these studies increase population productivity. In Chapter 3, we addressed this gap by leveraging two decades of data on cumulative restoration in nine tidal delta estuaries of Puget Sound and long-term monitoring of outmigrant juvenile Chinook salmon and returning adults for populations in those systems. The tidal deltas included in our study vary with respect to current and historical habitat extent and the timing, number, and areal extent of restoration efforts, as well as the abundance and life history diversity of the populations that use estuarine habitats. Most have not had consistent long-term monitoring of habitat change or long-term monitoring of juvenile salmon populations within tidal deltas.

Therefore, in Chapter 3, we produced spatial datasets to estimate changes in prime rearing habitat over time (Fig. 6, Appendix 3.1), and used habitat change data to test whether change in tidal deltas influenced productivity of Chinook populations. After controlling for larger scale temporal and spatial patterns, we found that smolt-to adult return (SAR) rates increased after estuary restoration. Importantly, the benefits of estuary restoration actions were not immediately detectable, but instead manifested ~4-9 years after restoration (Fig. 7). This lag is consistent with ecological theory and data showing that wetland recovery rates and habitat function take time to recover following restoration. We did not examine lag effects beyond 9 years due to limitations imposed by time series lengths; benefits may continue accruing with additional time. In addition, we found a negative relationship between SAR and outmigrants, suggesting that limited habitat availability may result in density-dependent population bottlenecks for estuarine-dependent life stages. The effect of restoration on SAR tended to be weaker in populations with higher proportions of fry migrants, which are also the larger populations. The results of our study indicate that estuary restoration can be an effective tool promoting progress toward recovery for listed populations, but suggest a protracted timeline for realization of potential benefits. Continued support for accelerating restoration, as well as ongoing monitoring of habitat and fish populations, will be critical for addressing restoration actions and population recovery. More broadly, these results suggest that given the time lags inherent in restoration of habitat function, societal patience is warranted in big experiments to reverse long trends in environmental degradation.

Summary

Our collection of studies provides the strongest evidence to date that estuary restoration benefits salmon at the population scale. Indeed, this work builds on other studies (David et al. 2014, Davis et al. 2019, Woo et al. 2018) to suggest that large, well-planned habitat restoration projects improve growth conditions in the tidal delta for juvenile Chinook salmon, and that these benefits have cascading effects not only through juvenile stages but to adulthood as well (Chapter 4). These findings are critical to 1) help provide benchmarks of success, 2) enable relative comparisons between estuary restoration and other types of management (e.g., limiting harvest, changing hatchery management), 3) improve design and prioritization of different restoration projects across Puget Sound, and 4) demonstrate to funders, managers, and stakeholders how estuary restoration is making a difference.

Some biological responses appear to follow immediately after restoration actions while others – namely survival rates, which are of particular interest – appear to materialize more slowly. Owing to concerted efforts to restore and monitor estuaries and the patience to allow restorative processes to unfold, our results align with the expectations of biologists working decades ago that estuaries provide important but degraded habitats and that salmon will benefit from their restoration (Simenstad et al. 1982). These studies also provoke additional questions (e.g., what are the most effective restoration designs? How resilient are cumulative estuary restoration efforts to climate impacts?) for which our findings just start to address. In Chapter 4, we provide context for our suite of studies and address how these additional questions can be examined in future studies.

Figure 6 (Chapter 3, Fig. 3). Time series of total prime rearing length (PRL) by delta. Note varying y-axis scales to improve visibility.


Figure 7 (Chapter 3, Fig. 6). Annual SAR of individual systems minus process error from top performing SAR model compared to changes in prime rearing length lagged seven years and proportion fry. Color/symbol combinations define different populations, and symbol size illustrates binned ranges in proportion fry. Line indicates a linear model fit to the raw data points shown.

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This page was last edited on 10 April 2025, at 21:35.
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