Recent studies have shown that the total nitrogen to total phosphorus (TN:TP) ratio and nitrogen oxidation state may have substantial effects on secondary metabolite (e.g., microcystins) production in cyanobacteria. We investigated the relationship between the water column TN:TP ratio and the cyanobacterial secondary metabolites geosmin, 2-methylisoborneol (MIB), and microcystin using multiple years of data from 4 reservoirs located in the Midwestern United States. We also examined the relationship between water column concentrations of chemically oxidized (NO₃) and reduced (NH₃) nitrogen, the NO₃:NH₃ ratio, cyanobacterial biovolume, and associated secondary metabolites. We found that the cyanobacterial secondary metabolites geosmin, MIB, and microcystin primarily occurred when the TN:TP ratio was <30:1 (by mass), likely due to higher cyanobacterial biovolumes at lower TN:TP ratios. We also found that relative cyanobacterial biovolume was inversely related to the NO₃:NH₃ ratio. Both N₂- and non-N₂-fixing cyanobacteria seemed to produce secondary metabolites and had higher concentrations per unit biovolume when NO₃:NH₃ ratios were relatively low. Our data thus are consistent with the hypothesis that lower TN:TP ratios favor cyanobacterial dominance and also suggest that relatively low NO₃:NH₃ ratios provide conditions that may favor the production of cyanobacterial secondary metabolites. Our data further suggest that increases in the absolute concentrations of TP or NH₃ (or both), causing decreases in TN:TP and NO₃:NH₃ratios, respectively, may stimulate cyanobacteria having the metabolic ability to produce geosmin, MIB, or microcystins. Future studies should address how the NO₃:NH₃ ratio affects phytoplankton community structure and occurrence and production of cyanobacterial secondary metabolites.