To identify the seasonal pattern of nitrogen (N) and phosphorus (P) limitation of phytoplankton in four different lakes, biweekly experiments were conducted from the end of March to September 2011. Lake water samples were enriched with N, P or both nutrients and incubated under two different light intensities. Chlorophyll a fluorescence (Chla) was measured and a model selection procedure was used to assign bioassay outcomes to different limitation categories. N and P were both limiting at some point. For the shallow lakes there was a trend from P limitation in spring to N or light limitation later in the year, while the deep lake remained predominantly P limited. To determine the ability of in-lake N:P ratios to predict the relative strength of N vs. P limitation, three separate regression models were fit with the log-transformed ratio of Chla of the P and N treatments (Response ratio = RR) as the response variable and those of ambient total phosphorus:total nitrogen (TN:TP), dissolved inorganic nitrogen:soluble reactive phosphorus (DIN:SRP), TN:SRP and DIN:TP mass ratios as predictors. All four N:P ratios had significant positive relationships with RR, such that high N:P ratios were associated with P limitation and low N:P ratios with N limitation. The TN:TP and DIN:TP ratios performed better than the DIN:SRP and TN:SRP in terms of misclassification rate and the DIN:TP ratio had the highest R2 value. Nitrogen limitation was predictable, frequent and persistent, suggesting that nitrogen reduction could play a role in water quality management. However, there is still uncertainty about the efficacy of N restriction to control populations of N2 fixing cyanobacteria.

Due to their competitive advantage when inorganic nitrogen (N) sources are scarce, it is widely assumed that the abundance and N2‐fixation rate of N2‐fixing cyanobacteria (Nostocales) would increase in response to reduced N loading. If realized, this response would render efforts to improve water quality by N reduction ineffective. To assess this, we performed a microcosm experiment using water from an N limited lake, Langer See, in which phosphorus loading was held constant, while a gradient of decreasing N loading was simulated. Nostocales biovolume increased over time in all microcosms, regardless of the N addition rate, so that no difference in Nostocales biovolume developed between high and low N microcosms. In contrast, the biovolumes of other taxa (especially non‐fixing cyanobacteria) were lower at low N addition rates. N2‐fixation increased in low N microcosms, compensating for 36% of the difference in N addition by day 6. However, this compensation rate was achieved at Nostocales biovolumes far higher than those typical in the studied lake. At biovolumes typical for summer the compensation rate would only account for 7% of the omitted N. If these results were to hold over longer time scales, in shallow polymictic lakes like Langer See, reduced N loading may lower both in‐lake N concentrations and biovolumes of non‐fixing phytoplankton without significantly impacting Nostocales biovolume.