San Francisco Estuary and Watershed Science

We used the UnTRIM San Francisco Bay–Delta hydrodynamic model to examine the spatial distribution of salinity as a function of freshwater flow in the San Francisco Estuary. Our particular focus was the covariation of flow with the spatial extent of the low-salinity zone (LSZ: salinity = 0.5 to 6), and with the extent of habitat for common species of -nekton as defined by their salinity ranges. The UnTRIM model has an unstructured grid which allowed us to refine earlier estimates of the availability of suitable salinity ranges, particularly for species resident in low salinity. The response of the salinity field to flow was influenced by the bathymetry of the estuary. Area and volume of the LSZ were bimodal with X2, the distance up the axis of the estuary to a near-bottom salinity of 2, roughly the middle of the LSZ. The smallest area and volume occurred when the LSZ was in the Delta or Carquinez Strait, moderate values when it was in Suisun Bay, and the highest values when it was in broad, shallow San Pablo Bay. Resource selection functions for the distributions of common nekton species in salinity space were up-dated from previous values and used to calculate salinity-based habitat indices using the UnTRIM results. These indices generally increased with decreasing X2 (increasing flow), but the slopes of these relationships were mostly inconsistent with corresponding relationships of abundance to flow. Thus, although the salinity range used by most nekton expands as flow increases, other mechanisms relating population size to flow are likely more important than the physical extent of suitable salinity.

Long-term hydrodynamic and salinity transport modeling of the Sacramento–San Joaquin Delta is needed to evaluate the future Delta in terms of the California co-equal goals of ecosystem health and reliable water supply. While 2-D and 3-D hydrodynamic and water quality models are by definition better suited to modeling a complex network of tidally influenced flows under future conditions, a 1-D model is more computationally efficient in narrowing the large variety of multiple-year simulations required into a more manageable task. Still, a 1-D model of sea level rise in an estuary must account for the three-dimensional effects where increased depths will affect density driven (baroclinic) circulation and tidal dispersion of salt. In this paper, we use a simplified Delta network model with a tidally averaged computational approach to quickly perform multi-year simulations for sea level rise. The 1-D model uses tidal dispersion coefficients developed from 3-D hydrodynamic models. The resulting model is capable of performing very fast simulations over a wide range of conditions, providing guidance on what should be explored in depth with more detailed, but slower models.

Comparisons of unimpaired Delta inflow with the historical case show that the south Delta and San Joaquin River would be much fresher without exports, while the Sacramento River would be fresher in spring and more saline in the fall. Sea level rise will increase salinity throughout the Delta over time. With peripheral conveyance of export, water salinity will intrude upstream in the Sacramento River, be slightly lower up the San Joaquin River and increase in the south Delta. With sea level rise, peripheral conveyance will have similar trends to changes to the historical case, but export salinity will be improved by the peripheral conveyance component. A larger peripheral conveyance can benefit both the ecosystem and exports if managed properly.

Recovery of fish with adipose fin clips (adc) and coded-wire tags (cwt) in escapement surveys allows calculation of expansion factors used in estimation of the total number of fish from each adc,cwt release group, allowing escapement to be resolved by age and stock of origin. Expanded recoveries are used to derive important estimates such as the total number and proportion of hatchery-origin fish present. The standard estimation scheme assumes accurate visual classification of adc status, which can be problematic for decomposing carcasses. Failure to account for this potential misclassification can lead to significant estimation bias. We reviewed sample expansion factors used for the California Central Valley Chinook salmon 2010 carcass surveys in this context. For upper Sacramento River fall-run and late fall-run carcass surveys, the estimated proportions of adc,cwt fish for fresh and non-fresh carcasses differed substantially, likely from the under-recognition of adc fish in non-fresh carcasses. The resulting estimated proportions of hatchery-origin fish in the upper Sacramento River fall-run and late fall-run carcass surveys were 2.33 to 2.89 times higher if only fresh carcasses are considered. Similar biases can be avoided by consideration of only fresh carcasses for which determination of adc status is relatively straightforward; however, restricting the analysis entirely to fresh carcasses may limit precision because of reduced sample size, and is only possible if protocols for sampling and recording data ensure that the sample data and results for fresh carcasses can be extracted. Thus we recommend sampling protocols that are clearly documented and separately track fresh versus non-fresh carcasses, either collecting only definitively adc fish or that carefully track non-fresh carcasses that are definitively adc versus those that are possibly adc. This would allow judicious use of non-fresh carcass data when sample sizes are otherwise inadequate.