Nitrogen pollution in the oligotrophic Chaihe Reservoir leads to reconsideration of whether nitrogen control is necessary. Does this mean that eutrophication control has the potential to create “cleaner lakes that are dirtier lakes?” The Chaihe Reservoir is a typical case of a water body with high nitrogen and low algal populations. The relationship between the chlorophyll a (Chla) and nutrients (total nitrogen [TN] and total phosphorus [TP]) in the reservoir was analyzed using the filtering trajectory method (FTM). The results showed that the Chaihe Reservoir recovered to an oligotrophic state after the TP concentration greatly decreased, but it faces a new dilemma of nitrogen pollution. This provides further empirical support for the role of phosphorus in controlling the nitrogen cycle and fate in freshwater ecosystems. The contour plot and Chla-TN/TP diagram indicated that a higher TN/TP contributed to a reduction in Chla. The thresholds for TP and TN in the reservoir were proposed using the double probability method (DPM). It is recommended to remove nitrogen at the end of a drinking water supply system due to the nitrogen pollution of the Chaihe Reservoir. The TN threshold for buffering control provides a quantitative basis for implementing a nutrient management plan.