Modeling of fate and transport in San Francisco Bay is needed to address many priority management questions that have been articulated by RMP workgroups for PCBs, sediment, and contaminants of emerging concern (CECs). This report is part of a first phase of implementation of a multi-year workplan for in-Bay modeling. For both PCBs and CECs, understanding fate in margin areas that receive stormwater inputs is a high priority information need. The first phase of this multi-year project is developing an overall model for the Bay, but with an initial focus on San Leandro Bay (SLB), a margin area of interest for both PCBs and CECs. Later phases of the multi-year workplan will include further development of a whole-Bay model, a model for a second Priority Margin Unit (PMU) (Steinberger Slough), and an updated food web model for PCBs. The lessons learned from the smaller-scale studies will inform development of the large-scale modeling framework to address Bay-wide management questions.