Floods of coastal cities can transport contaminants, including excess nutrients, into adjacent estuaries. The extent to which the delivery of this material impacts biogeochemistry and water quality depends on when and where concentrations of contaminants are high. This is complicated to predict, in part due to variations in precipitation, local winds, and water levels among different storms. Additionally, the magnitude and timing of precipitation, winds and water levels changes due to decadal and longer-term variations in climate. This presentation will focus on how the transport of contaminants is influenced by the relative timing and magnitude of river discharge, winds and other ocean processes, as well as the location at which they enter the estuary. This work is being done as part of a project 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, before consideration of other locations. For this presentation 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 (e.g. from different rivers and other point sources) 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, wind direction and magnitude, 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.