Abstract Biscayne Bay is a naturally clear-water bay that spans the length of Miami-Dade County, Florida, USA. It is bordered on the east by barrier islands that include Miami Beach and is an almost completely urban bay in the north and a relatively natural bay in the south. Planned water management changes in the next few years may decrease freshwater flows to the bay from present sources, while offering reclaimed wastewater in return. In addition, a project is planned to restore the former diffuse freshwater flow to the bay through many small creeks crossing coastal wetlands by redistributing the water that now flows into the bay through several large canals. To guide a science-based, adaptive-management approach to water-management planning, a conceptual ecological model of Biscayne Bay was developed based upon a series of open workshops involving researchers familiar with Biscayne Bay. The CEM model relates ecological attributes of the bay to outside forcing functions, identified as water management, watershed development, and sea-level rise. The model depicts the effects of these forcing functions on the ecological attributes of the bay through four stressors. The hypothesized pathways of these effects include salinity patterns, water quality, sediment contaminant concentrations, and physical impacts. Major research questions were identified with regard to uncertainties explicit in the model. The issues addressed include, for example (1) the quantitative relationship between upstream water management, rainfall, and flow into Biscayne Bay; (2) the salinity gradient required to restore the historical estuarine fish community; (3) the potential effect of freshwater inputs on benthic habitats; (4) the effect of introduced nutrient and contaminant loads, including the effects of reclaimed wastewater.