Previous research suggests that fertilization of surface waters with chemically reduced nitrogen (N), including ammonium (NH4+), may either enhance or suppress phytoplankton growth. To identify the factors influencing the net effect of NH4+, we fertilized natural phytoplankton assemblages from two eutrophic hardwater lakes with growth-saturating concentrations of NH4Cl in 241 incubation experiments conducted biweekly May–August during 1996–2011. Phytoplankton biomass (as chlorophyll a) was significantly (p < 0.05) altered in fertilized trials relative to controls after 72 h in 44.8% of experiments, with a marked rise in both spring suppression and summer stimulation of assemblages over 16 yr, as revealed by generalized additive models (GAMs). Binomial GAMs were used to compare contemporaneous changes in physico-chemical (temperature, Secchi depth, pH, nutrients; 19.5% deviance explained) and biological parameters (phytoplankton community composition; 40.0% deviance explained) to results from fertilization experiments. Models revealed that that the likelihood of growth suppression by NH4+ increased with abundance of diatoms, cryptophytes, and unicellular cyanobacteria, particularly when water temperatures and soluble reactive phosphorus (SRP) concentrations were low. In contrast, phytoplankton was often stimulated by NH4+ when chlorophytes and non-N2-fixing cyanobacteria were abundant, and temperatures and SRP concentrations were high. Progressive intensification of NH4+ effects over 16 yr reflects changes in both spring (cooler water, increased diatoms and cryptophytes) and summer lake conditions (more chlorophytes, earlier cyanobacteria blooms), suggesting that the seasonal effects of NH4+ will vary with future climate change and modes of N enrichment.