The Sacramento River Bank Protection Project protects levees and flood control structures along the Sacramento, American, and Feather Rivers. These habitat alterations to these rivers and associated flood plains can affect resident fish populations including three threatened or endangered salmonids and a threatened population of green sturgeon. Bank protection projects can have multiple effects on the riverine system including geomorphic, hydraulic, vegetative, benthic substrate, sediment budget and habitat complexity changes.

This project is to develop a model to analyze the effects of back protection in the above mentioned areas. We are developing a spatially explicit agent based model (ABM) that links bathymetry, hydrology, and water and habitat quality to population-level responses of focal species. The model will function for both riverine and floodplain areas and both salmonids and sturgeon. The end product will have a simple GUI where the user will only need to input parameter values and select input files.

Green Sturgeon Side Scan Sonar

Green Sturgeon Census

The threatened southern population of green sturgeon spawn on an upper section of the Sacramento River. Estimating the abundance and its trajectory is crucial for the species to recover. We conduct an annual spawner survey using acoustic imagery (DIDSON and side scan sonar). We use a combination of telemetry data, matrix modeling, and statistical techniques to estimate a total population from this spawning data. We also investigate how this species uses habitat on a reach and sub reach scale.

ABM IBM Salmon Sacramento River inSALMO

Restoration Assessment

There are a large amount of past, active, and proposed fish habitat restoration projects in California’s Central Valley (and on many watersheds worldwide). These restoration activities are diverse and any one action will often have numerous, complex effects on the resident fish populations. As such, to evaluate these restoration actions we need tools and models which are capable of assessing both a diverse set of habitat alterations and the resulting effects. Agent based models (ABMs) are an excellent framework for these problems as they can explicitly use inputs that represent the habitat alteration and also account for numerous, complex interactions between the resident fish populations and the habitat. We both use and alter existing ABMs (including inSALMO) to assess the effect of habitat restoration of the endangered winter-run Chinook on the Sacramento River. With these models we can look at a diverse set of potential effects from fish abundance and individual size, to the risk from predation and habitat resident time. This information can help inform and improve habitat alteration and restoration actions.



Winter-run Chinook, like many anadromous species, have a dam blocking their historical spawning grounds. This is particularly detrimental to winter-run Chinook as their eggs must endure the warm summer temperatures of the Central Valley. This restricted habitat makes the eggs vulnerable to temperature dependent mortality, which is a complex interaction of metabolic rate, oxygen uptake, and interstitial flow.

Causes of temperature dependent mortality are difficult to experimentally investigate. We have developed algorithms to both construct simulated redds and use computational fluid dynamics to investigate mechanisms of temperature dependent egg mortality in salmon redds.