A Geographic Information System (GIS)-aided flow-tracking technique was adopted to investigate nutrient exchange rates between specific benthic communities and overlying seawater in a fringing reef of Ishigaki Island, subtropical Northwestern Pacific. Net exchange rates of NO3-, NO2-, NH4+, PO43-, Total-N and Total-P were estimated from concentration changes along the drogue trajectories, each of which was tracked by the Global Positioning System and plotted on a benthic map to determine the types of benthic habitat over which the drogue had passed. The observed nutrient exchange rates were compared between 5 typical benthic zones (branched-coral (B) and Heliopora communities (H), seaweed-reefrock zone (W), bare sand area (S), and seagrass meadow (G)). The dependence of nutrient exchange rates on nutrient concentrations, physical conditions and benthic characteristics was analyzed by multiple regression analysis with the aid of GIS. The spatial correlation between nutrient exchange rates and benthic characteristics was confirmed, especially for NO3- and PO43-, which were usually absorbed in hydrographically upstream zones B and W and regenerated in downstream zones H and G. NO3- uptake in zones B and W was concentration-dependent, and the uptake rate coefficient was estimated to be 0.58 and 0.67 m h-1, respectively. Both nutrient uptake in zone W and regeneration in zone H were enhanced in summer. The net regeneration ratio of NO3-/PO43- in zone H in summer ranged 5.2 to 34 (mean, 17.4), which was somewhat higher than previously measured NO3-/ PO43- for sediment pore waters around this zone (1.1-8.5). Nutrient exchanges in zone S were relatively small, indicating semi-closed nutrient cycling at the sediment-water interface of this zone. NH4+ efflux from sediments was suggested in zone G. The data suggest that the spatial pattern of nutrient dynamics over the reef flat community was constrained by zonation of benthic biota, and that abiotic factors such as nutrient concentrations and flow rates, influenced nutrient exchange rates only in absorption-dominated communities such as zones B and W. © The Oceanographic Society of Japan/TERRAPUB/Springer 2007.