Lakes provide various ecosystem services that support biotic habitats and human life. In contrast, many lakes in the world are degraded due to pollutant supply from surrounding areas and human activities in the lake. Lake Toba, which is the largest lake in Indonesia, has indicated a polluted condition. However, the source and load of each pollutant are not yet known. A study has been conducted to determine nutrient and organic load levels entering the lake represented by Total Phosphorus (TP) and Chemical Oxygen Demand (COD), respectively. Observations were carried out in November 2017 at 22 locations, i.e., at 12 inlet rivers debouching to the lake and 10 sites at the lake. The pollutant impact was assessed from water class criteria based on COD, waters trophic status based on TP, and vertical oxygen profile representing cage aquaculture (CA) and non-cage aquaculture (NCA) areas. Based on COD and government regulation number 82/2001, water quality at the lake inlets was class III and IV. In the lake area, water class in NCA was III, while in CA the water class tends to be III and IV. Estimated TP loading from the catchment area was 138 tonnes/yr, while that from cage aquaculture activity was 570.33 tonnes/yr. Pollutants have caused the worsening of water class, increasing water column anoxia in the hypolimnion layer and eutrophication in Lake Toba.