Temperature and Tidal Dynamics in a Branching Estuarine System

California's Sacramento-San Joaquin Delta (the Delta) will experience tremendous change in the coming decades, as natural variation within the Delta confront wholesale background changes due to climate change, water shortages, potential levee failures, invasive species introduction, and anthropogenic management decisions. In light of this, I present work analyzing a number of facets of the Delta's physical functioning and how they might affect its ecological function. Using a simple statistical water temperature model, we project water temperatures to warm across the region in the coming century, threatening species near ecological bottlenecks, and stressing other native populations. For example, timing of spring spawning temperatures for Delta smelt will shift earlier in the year. Lethal temperatures for Delta smelt will be more frequent in all four climate scenarios tested. I discuss possibilities for managing the Delta's thermal regime. I did field observations in Cache Slough in the north Delta to parse out smaller scale water temperature variations within a shallow tidal slough. Given bathymetric variation, velocity and thermal gradients develop, which mix and move throughout this complex region. These gradients can intensify near intersections, mixing out over tidal and diurnal cycles. Bathymetric variation combined with atmospheric heating/cooling create thermal gradients. Advection and diffusion move these gradients, which can be intensified where channel merge. Sharp gradients matter biologically; they also create possibilities for refugia for species pushed to their thermal limits. These gradients affect lateral flows, but lateral flows are more strongly affected by lateral wind forcing. Lateral circulation from wind is not strong enough to affect along-channel thermal mixing, as along-channel forcing is strong enough to overcome the homogenization driven by these lateral circulations.In branching tidal systems, tidal dissipation, propagation and reflection together define the spatial distribution of tidal energy. When specific locations or regions are altered, for example through the restoration of tidal marsh, there is uncertainty as to how the system will respond, including the spatial influence of the changes. When tidal marsh habitat is restored, it creates local tidal dissipation which may alter tidal energy in other parts of the estuary, potentially altering the function of tidal marshes elsewhere. I present results of a simple analytic model of tidal propagation in a branching system. I developed wave equations for along-channel velocity and wave height which account for friction and changes in channel geometry. By linearizing the friction term in the depth-averaged along-channel momentum equation and including an amplification factor in the wave form, then combining it with the continuity equation, I solved for wave speed and amplification as a function of friction and channel geometry. I also solved for the tidal velocity and stage as a function of position and time. Using this solution within an idealized branching channel estuary and applying matching conditions at the branches, I analyzed the effects of changes to one branch on tidal regimes throughout an idealized branching channel estuary. I then applied this simple model to consider restoration questions on California's Sacramento-San Joaquin Delta.