To elucidate the anthropogenic nutrient load, nitrate + nitrite and phosphate concentrations were measured at an upstream point where there is little tidal change in the Miyara River, Ishigaki Island, Japan. The environmental conditions of lower trophic level production were observed, and factors related to the relatively high coral cover rate were investigated on the reef slope, although there have been heavy loads on the reef flats and inside the reef edge of Miyara Bay. Though the nitrate + nitrite load was always high, the environmental conditions for lower trophic level production were found to be within an appropriate range for coral growth.