Measurements of the distribution patterns of nutrients (ammonium, nitrate, orthophosphate, total N and total P) and chlorophyll concentrations were conducted under an interdisciplinary program known as SEAKEYS, initiated because of concern that anthropogenic nutrients may be impacting Florida coral reefs. Samples were collected along transects that extended from passes or canals to 0.5 km offshore of the outermost reefs. Seven of the transects were either in the Biscayne National Park (BNP) and Key Largo (upper keys) or Seven Mile Bridge/Looe Key (upper part of lower keys) areas, which have the best present-day reef development; the two in the middle keys off Long Key were in an area of minimal reef development where passes allow estuarine Florida Bay water to flow onto the Florida reef platform. Off the upper keys, water column concentrations of N and chl a were elevated near marinas and canals (1 μM NO3, 1 μg/l chl a), but returned to oligotrophic levels (e.g., chl a ⩽ 0.25 μg/l; NO3 ⩽ 0.25 μM; NH4 ⩽ 0.10 μM) within 0.5 km of shore. Phosphorus concentrations, however, were often higher offshore ⩾ 0.2 μM PO4). Sediment interstitial nutrient concentrations decreased from inshore to the offshore reef areas (e.g., ⩾ 100 μM NH4 inshore to ⩽ 50 μM NH4 offshore) and were comparable to those of some presumably pristine coastal and reef carbonate sediments. Sediment bulk N was higher nearshore and decreased steeply offshore ( ⩾ 60 μg-at N/gm sediment to ⩽ 20 μg-at N/gm sediment, respectively); bulk P concentrations (⩽ 6 μg- at P/gm sediment) varied little or exhibited the reverse pattern. Sediment N:P ratios were consistently lower offshore (1 10 vs. 20 40 nearshore). Higher offshore P concentrations are attributed to periodic upwelling along the shelf edge. In the middle keys water column nutrients and chl a concentrations were both higher than those in the upper keys, and there was less of an inshore-offshore decrease than that noted in the upper keys. Sediment nutrients were higher also, and nearshore and offshore areas did not differ. Water column and sediment nutrient concentrations and distribution patterns in the upper part of the lower keys were most similar to those measured in the upper keys. Overall, the present data do not support the contention that reef areas in the upper keys are accumulating elevated loads of land-derived nutrients via surface water flow, but does document moderately elevated nutrient and chl a levels in many developed nearshore areas. Most of the anthropogenic and natural nutrients entering the coastal waters from shore appear to be taken up by near shore algal and seagrass communities before they reach patch reef areas. Further work is needed to determine whether nutrient-enriched ground waters reach the reefs, however these would be expected to cause an enrichment of reef sediments, which was not observed.