As external nutrients inputs above a critical level may drive shallow lakes to shift from clear water to a turbid state, it is important to detect ecological changes of the lake at an early stage of the eutrophication process. In this way, it is possible to assess the stress tolerance of the system and thereby improve the possibilities for proper management. In this study, water quality parameters and the biomass of submerged macrophytes were examined monthly in two bays receiving contrast amounts of nutrient input of a large mesotrophic lake from August, 2011 to July, 2012. We found that effects of external nutrient input could not be explained by differences between the two bays in water quality parameters, such as total nitrogen, total phosphorus, chlorophyll a, light attenuation coefficient and water transparency (Secchi depth), but by the species composition and temporal variation of submerged vegetation. In the progress of eutrophication, the submerged macrophyte community changed from Potamogeton maackianus dominance to co-dominance of Ceratophyllum demersum and P. maackianus, and became more seasonally variable in biomass and coverage due to the shorter survivorship of C. demersum. We suggest that in the early stage of eutrophication, when submerged macrophytes are still abundant, water quality parameters should be coupled with monitoring of submerged vegetation to examine the effects of external nutrient loading on shallow lake ecosystems.