This study was carried out to elucidate the relation between water quality and structure of the aquatic ecosystem in the agriculture reservoir Otae-ji from January to December in 2009. The proportion of forest was 46.98%, which means that non-point sources are major contributor of water pollution in this area. The annual mean COD(Chemical Oxygen Demand) in Otae-ji was $3.6mgL^{-1}$, indicating, level II of environmental standards and the trophic state was mesotrophic. Although total phosporus concentration in the reservoir was high in August due to large inflow of nutrients from outside the reservoir during monsoon season, there was no break out of significant algal bloom in the summer. The seasonal succession of phytoplankton showed that the dinophyta dominated in the the spring, chlorophyta in the summer, chrysophyta and chlorophyta in the autumn and chrysophyta in the winter. In case of zooplankton, rotifers dominated in the most seasons, but cladoceran(Bosmina longirostris) dominated in June and copepod(Nauplii) in August. The macrophyte plants showed diverse species compositon consisted of 3 varieties, 24 species, 23 genera, 15 families and 14 orders. The macroinvertebrates also showed various FFG(Functional Feeding Groups) such as GC(Gathering-Collector), P(Predator), SH(Shedder), FC(Filter-Collector) and PP(Plant-Piercer). Ecosystem stability analysis using aquatic insects was classified as Group I, which has high resilience and resistance indices. A total of 14 species of fish was collected but exotic species such as Lepomis macrochirus and Micropterus salmoides were not found in Otae-ji. In conclusion, the preservation of healthy food wed in the reservoir ecosystem is closely related to water quality management as well as effective prevention of algal bloom by helping good material circulation in aquatic ecosystems.