At Sekisei Reef in southwestern Japan (24° N), coral cover dramatically decreased in the mid-1980s, probably due to a population outbreak of the coral predator Acanthaster planci. Coral communities subsequently recovered well outside the semiclosed lagoon, but recovery has been poor inside it. Hence, water-quality degradation including eutrophication has been a concern inside the lagoon. In addition, temporal variation in eutrophication parameters is common among high-latitude coral reefs, resulting in difficulties in evaluating them. Therefore, to address these issues, we monitored temperature, salinity, turbidity, chlorophyll-a, NOx-N (NO3-N + NO2-N), and NH4-N concentrations year-round across the lagoon at Sekisei Reef. Turbidity and NOx-N concentration increased with increasing wind velocity, suggesting that variation in turbidity and NOx-N concentrations was attributed to resuspension of bottom sediments, and NOx-N release through regeneration processes of micro-organisms from the sediments and reef frameworks, respectively. In contrast, variation in chlorophyll-a and NH4-N concentrations appears to be mainly controlled by the seasonality of temperature and irradiance. Long retention time of seawater inside the lagoon seems to have enhanced NH4-N assimilation and increase of phytoplankton during summer. Inside the lagoon, turbidity, NOx-N, and summer chlorophyll-a concentrations were higher, and variation in temperature was larger than outside it. Although water quality appears not to be seriously degraded, multiple effects of these water-quality variables might have negatively affected recovery of coral communities inside the lagoon. Recent expansion of land use on nearby islands might have contributed to water-quality degradation inside the lagoon.