The serious lake eutrophication has drawn increasingly attention, requiring further and deeper knowledge to understand its restriction factors of pre-disturbance conditions or historical reference conditions. In the meanwhile, Lake Nutrient Reference Conditions (LNRCs) are important indicators of eutrophication but hardly determined in the presence of eutrophication. In this research, a novel extrapolation approach was raised to determine LNRCs and its impacts on eutrophication, with the integral model of Optimal Map Recognition (OMR) and Pattern Recognition Inverse Mapping (PRIM). Validated with public data and experimental simulation, the approach was suggested as a reliable extrapolation for LNRCs determination. Further case study on Dianshan Lake and Chenghai Lake applied the novel extrapolation model in real eutrophication estimation and prediction, the results of which were in good agreement with those deduced by other techniques.