Coral reefs are vibrant, productive ecosystems that face a variety of threats, including disease, temperature stress and pollution. In order to effectively manage coral reef resources, adequate data are required to assess status and track change in these systems. The state of Florida has over 100 linear miles of coral reefs north of Miami that, unlike the Florida Keys, have not historically had a continuous water quality monitoring program. Thanks to a robust new federal-state partnership water samples are being collected monthly at 115 sites and being analyzed for total suspended solids, nitrate, nitrite, ammonium, urea, total nitrogen, orthophosphate, total phosphorus and silicate. Targeted samples were collected around the inlets and WWTP outfalls (where present) to capture the sources of pollutants to the coastal waters. Samples were also taken at stratified random sites on the reefs in order to capture the ambient water quality characteristics of the reefs themselves. The inlets and outfalls stand out as clear (statistically significant) point sources of pollutants, but vary by pollutant, e.g. the outfall contributes primarily ammonium, whereas the inlets contribute TSS and phosphorus and oxidized nitrogen. The reef sites generally had lower levels of nutrients and TSS, but showed periods of elevated pollutants, such as after storm events. The genesis of this monitoring program for the Southeast Florida Reefs would not have been possible without the federal-state partnership. The data will be useful to coastal managers for evaluating the efficacy of management actions and tracking water quality changes over time.