Climatic changes and anthropogenic activities could affect nutrients’ status significantly in the different lake ecosystems. Nutrients in Lake Hulun and Lake Taihu, two largest shallow cyanobacteria-blooming lakes in northern and southern China, respectively, were at eutrophicated levels in 2009. The concentrations of total nitrogen and total phosphorus were 3.346 and 2.250 mg/L as well as 0.435 and 0.062 mg/L, respectively, in these two lakes with different causes of eutrophication. For Lake Hulun, it was the decreased amount of water as a result of the warming and drying climate that accounted for the abrupt increase of total nitrogen and total phosphorus levels through inspissation. In addition, the icebound effects, no outflows, low nutrients sequestration by the sediment and the reduction of aquatic productivity made the situation even worse. On the contrary, high population densities, the rapid development of agriculture and industry as well as urbanization have increased the nitrogen and phosphorus loads on Lake Taihu. Therefore, higher criteria of total nitrogen and total phosphorus should be applied in Lake Hulun given the difficulties in controlling climatic changes while much more rigorous standards should be established for Lake Taihu since the anthropogenic impacts on nutrient status are relatively easy to control.