Many important transitions in phytoplankton composition of lakes and oceans are related to shifts in nutrient supply ratios. Some phytoplankton transitions, such as cyanobacteria blooms in freshwater supplies and red tides in coastal oceans, are important for aquatic resource management. Therefore, it would be useful to have leading indicators which precede phytoplankton shifts and could be readily monitored in the field. We investigated potential indicators using a well-understood model of phytoplankton dynamics parameterized to mimic the transition toward cyanobacteria blooms in freshwater lakes. In stationary distributions, performance of the indicators depends on whether the species are capable of stable coexistence over a certain range of nutrient inputs. In transient simulations, however, indicators show consistent responses regardless of the possibility of stable coexistence. Leading indicators occurring 10 to 40 days prior to species shift include shift of lag-1 autoregression coefficient toward 0, low standard deviation, fluctuating skewness, and high kurtosis. These responses are different from those reported for critical transitions such as fold bifurcations. Thus, the indicators reveal clues to the mechanisms of important ecosystem transitions. In practice, indicators should be measured for multiple ecosystem variables, and interpretation of the indicators should be guided by experiments and mechanistic site-specific models to help resolve potential ambiguities.