Floods of coastal cities can transport contaminants and excess nutrients into adjacent estuaries. Predicting the transport of this material and its impact on biogeochemical processes is complicated by the many processes involved, ranging from storm characteristics to chemical reactions. This motivates the use of numerical models to understand the role of different processes on water quality during and following floods. This presentation will focus on new project that is using models to understand predictability of water quality during and following floods, focusing on the Patapsco and Back River estuaries that surround the coastal urban center of Baltimore, USA. Specifically, a numerical hydrodynamic model is being implemented using the Regional Ocean Modeling System (ROMS) that accounts for processes such as river discharge, winds, and larger scale circulation. Analysis of model results will focus on how the path of Lagrangian tracers originating in different portions of the domain varies in response to changes in river discharge, winds, and conditions in the Chesapeake Bay. The fate of Lagrangian tracers is expected to depend on the path of the river plume, as well as the location and time that the contaminant enters the estuary. Future work will include implementing hydrodynamic-biogeochemical coupling within ROMS to better understand variability in the transport of excess nutrients, as well as water quality impacts.