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Annual-scale environmental and ecosystem changes since the mid-19th century were reconstructed in a seasonally frozen lagoon, Lake Mokoto, located along the Okhotsk Sea coast of Hokkaido, northern Japan. X-ray fluorescence (XRF) and diatom analyses of laminated sediment were conducted to determine the impact of short-term climate oscillations and anthropogenic eutrophication on the lagoon ecosystem. In this lagoon, eutrophication has progressed since the early 20th century due to deforestation and human activity in the catchment area, such as development of the cattle industry and field agriculture. In particular, the sedimentation rate of Lake Mokoto and potassium and phosphorus contents of lake sediment have increased rapidly since 1970, in association with an increase in the number of cattle. In addition, the Lake Mokoto ecosystem shows inter annual and decadal cyclic fluctuations that are separate from the anthropogenic effects. Prior to anthropogenic eutrophication, the nutrient condition of Lake Mokoto showed a close relationship with the Pacific decadal oscillation (PDO). The growth of seagrass, inferred from epiphytic diatom abundance, showed a clear decadal cycle following variation in solar irradiance.