A simulation method for combining hydrodynamic data and acoustic tag tracks to predict the entrainment of juvenile salmonids onto the Yolo Bypass under future engineering scenarios

During water year 2016 the U.S. Geological Survey California Water Science Center (USGS) collaborated with the California Department of Water Resources (DWR) to conduct a joint hydrodynamic and fisheries study to acquire data that could be used to evaluate the effects of proposed modifications to the Fremont Weir on outmigrating juvenile Chinook salmon. During this study the USGS surgically implanted acoustic tags in juvenile late fall run Chinook salmon from the Coleman National Fish Hatchery, released the acoustically tagged juvenile salmon into the Sacramento River upstream of the Fremont Weir, and tracked their movements as they emigrated past the western end of the Fremont Weir.

The USGS analyzed tracking data from the acoustically tagged juvenile salmon along with detailed hydrodynamic data collected in the Sacramento River during the winter/spring of water year 2016 in the vicinity of the western end of the Fremont Weir to assess the potential for enhancing the entrainment of Sacramento River Chinook salmon onto the Yolo Bypass under six different Fremont Weir modification scenarios. Each modification scenario consists of a notch or multiple notches in the Fremont Weir which are designed to divert a portion of the Sacramento River onto the Yolo Bypass when the Sacramento River is below the crest of the Fremont Weir. The primary goal of this entrainment analysis was to investigate how the location of the notch or notches in each scenario affected the entrainment of juvenile Chinook salmon onto the Yolo Bypass, and to predict the notch location or locations that would result in maximum entrainment under each modification scenario.

Stumpner et al.’s (in review) analysis of hydraulic data collected during the 2016 study period showed that backwater effects in the Sacramento River created significant variability in the relationship between Sacramento River stage and the proportion of the Sacramento River flow that we expect to be diverted onto the Yolo Bypass under the modification scenarios. Because of this variability, accurately evaluating the entrainment potential of possible notch locations for each scenario required combining historic abundance data for juvenile Sacramento River Chinook salmon with historic hydraulic data for the Sacramento River in the vicinity of the Fremont Weir, so that the entrainment estimates would reflect the covariance between Sacramento River stage, Sacramento River discharge, and juvenile salmon abundance within the historic record.

We used a Monte Carlo simulation framework to combine the high resolution hydrodynamic data and acoustic tag track data collected in 2016 with historic juvenile salmon abundance, Sacramento River stage, and Sacramento River discharge data from a period spanning water years 1996-2010 to assess the entrainment potential of different weir modification scenarios under historic conditions. The scenarios we simulated consisted of four single notch configurations, and two multiple notch configurations in the vicinity of the western end of the Fremont Weir. For each notch configuration the 15-water-year entrainment simulation was repeated for 63 possible notch locations in the vicinity of the western end of the Fremont Weir. This approach allowed us to assess the effect of notch location on the entrainment of juvenile salmonids onto the Yolo Bypass for each of the six notch configurations that we evaluated.

The entrainment simulations showed that the location of each notch configuration had a major impact on the entrainment for each scenario; the predicted entrainment of some scenarios varied by as much as 400% based on where the notch (or notches) was (were) located in the study area. All of the single notch scenarios performed best when they were located within a 330 ft (100 meter) long section of the Sacramento River bank adjacent to the western terminus of the Fremont Weir (Table 1). Both of the multiple notch scenarios performed best when their upstream notches were located about 660 ft (200 meters) upstream of the western terminus of the Fremont Weir (Table 1). The results of the entrainment simulations indicated that for each notch configuration the same notch location produced near-maximum entrainment regardless of run abundance timing; this result suggests that there are areas within the study are where a notch (or notches) can be sited to achieve maximum entrainment for all runs (barring significant behavioral or physiological differences between runs). In addition, the simulation results indicate that for each notch configuration the same location is expected to produce nearmaximum entrainment for both wet water years and dry water years.

Based on the results of the entrainment simulation we make three general recommendations for strategies to improve the entrainment potential of a notch in the Fremont Weir:

1) Comparisons between the maximum entrainment potential for each scenario suggested that total entrainment of winter run, spring run, and fall run salmon onto the Yolo Bypass can be increased by increasing the amount of water entering a notch when the Sacramento River stage is between 19 ft and 22 ft NAVD88; this could be accomplished by lowering notch invert elevations or by adding a control section to the Sacramento River to raise stage for a given discharge.

2) The relationship between Sacramento River stage and entrainment for each scenario indicated that entrainment efficiency for each scenario declined significantly once Sacramento River stage exceeded bankfull (approximately 28.5 ft NAVD88). This effect was likely due to inundation of the floodplain between the Sacramento River and the Fremont Weir; Stumpner et. al (In Review) have documented a reduction in the strength of the secondary circulation and centralization of the downwelling zone in the Sacramento River when this floodplain is inundated. Therefore, increasing the height of the river right bank of the Sacramento River to coincide with the height of the Fremont Weir is recommended to increase entrainment at higher stages.

3) Bathymetric features upstream of notch openings appeared to have a major impact on the entrainment potential of the simulated notches. For this reason we recommend taking care to avoid siting notches immediately downstream of bank features that alter the sidewall boundary layer, and we expect that smoothing the bank bathymetry upstream of a notch will enhance entrainment.

Finally, we caution that the entrainment simulation was based on the behavior of large hatchery smolts, so it is likely that our results will be sensitive to any differences in behavior and physiology between these hatchery surrogates and naturally migrating juvenile salmon.