Suspended sediment and nutrient loadings from agricultural watersheds have lead to habitat degradation in Lake Takkobu. To examine their relationships with land-use activities, we monitored sediment, nutrient and water discharges into the lake for a 1-year sampling period. The Takkobu River contributed the largest portion of the annual water discharge into the lake, compared with the other tributaries. During dry conditions, lake water flowed into the Kushiro River, and conversely during flooding, Kushiro River water flowed into the lake. Inflows from the Kushiro River had a high proportion of inorganic matter, with high concentrations of total nitrogen and total phosphorus, attributed to agricultural land-use development and stream channelization practiced since the 1960s in the Kushiro Mire. Nutrient loadings from these two rivers were significantly higher during flooding than in dry conditions. However, there was no clear correlation between river discharge and nutrient concentrations. Since land-use activities in the Kushiro River and Takkobu River watersheds were concentrated near rivers, nutrients easily entered the drainage system under low flow conditions. In contrast, water discharged from small, forest-dominated watersheds contained a low proportion of inorganic matter, and low nutrient concentrations. The suspended sediment delivered to the lake during the sample period was estimated as approximately 607 tons, while the total nitrogen and total phosphorus inflows were about 10,466 and 1,433 kg, respectively. Suspended sediment input into the lake was 65%, and total nitrogen and total phosphorus were 40% and 48%, respectively, being delivered by the Kushiro River.