Productivity, nutrient input, nutrient uptake, and release rates were determined for a coral-dominated reef flat at La Réunion, France, to assess the influence of groundwater nitrogen on carbon and nutrient budgets. Water samples were collected offshore in the ocean, at the reef crest and back reef for nutrients, picoplankton, pH, and total alkalinity. Volume transport of ocean water across the reef flat was measured using both current meters and drogues. Groundwater advected onto the reef flat and mixed with incoming ocean water. Metabolic rates for the reef community were determined to be: gross primary production = 1,000 mmol C m−2 d−1, community respiration = 960 mmol C m−2 d−1, and community calcification = 210 mmol C m−2 d−1. Across the reef flat, silicate behaved conservatively, there was net uptake of phosphate (0.06 mmol P m−2 d−1) and net release of nitrate, ammonia, dissolved and particulate organic nitrogen (total 7.0 mmol N m−2 d−1). Groundwater nitrate contributed 37% of the increase in nitrate plus ammonia. The first-order mass transfer coefficient of phosphate was 3.3 m d−1, and for nitrate plus ammonia, 5.9 m d−1. Gross N and P uptake from estimates of mass transfer and uptake of particles were 0.37 mmol P m−2 d−1 and 7.2 mmol N m−2 d−1, respectively giving an N:P uptake ratio of 20:1. Thus, the elevation of nitrogen across the reef flat maintains a high N:P flux, enhancing algal growth downstream of the transect. We conclude that net community production (40 mmol C m−2 d−1) was sustained by net uptake of phosphate from the ocean and net uptake of new nitrogen from groundwater.