Understanding the limiting factors of phytoplankton growth and competition is crucial for the restoration of aquatic ecosystems. However, the role and synergistic effect of co-varying environmental conditions, such as nutrients and light on the succession of phytoplankton community remains unclear. In this study, a hydrodynamic-ecological modeling approach was developed to explore phytoplankton growth and succession under co-varying environmental conditions (nutrients, total suspended solids (TSS) and variable N:P ratios) in a large shallow lake called Lake Chagan, in Northeast China. A phytoplankton bloom model was nested in the ecological modeling approach. In contrast to the traditonal ecological modeling, competition between phytoplankton species in our study was modeled at both the species/functional group and phenotype levels. Six phytoplankton functional groups, namely diatoms, green algae, Anabaena, Microcystis, Aphanizomenon and Oscillatoria and each of them with three limitation types (i.e., light-limitation, nitrogen-limitation and phosphorus-limitation) were included in the bloom model. Our results demonstrated that the average biomass proportion of the three limitation types (light-limitation, nitrogen limitation and phosphorus-limitation) in the six phytoplankton function groups accounted for approximately 50%, 37% and 23% of the total phytoplankton biomass, respectively. TSS suppressed the growth of diatoms and green algae, but favored the dominance of cyanobacteria in Lake Chagan, especially in the turbid water phase (TSS > 60 mg/L). In addition, it was reported that the potential of either N-fixing or non-N-fixing cyanobacterial blooming along the gradients of N:P ratios could exist under the influence of the co-environmental factors in the lake. The proportion of non-N-fixing cyanobacteria (i.e., Microcystis and Oscillatoria) exceeded the proportion of N-fixing cyanobacteria (i.e., Anabaena and Aphanizomenon) when the N:P ratios exceeded 20. Non-N-fixing cyanobacteria would become dominant at higher TSS concentrations and lower light intensities in the turbid water. N-fixing cyanobacteria favored lower N:P ratios and higher light intensities in the clearwater phase (where TSS < 60 mg/L). To sustain a good ecological status in the lake, our results suggest that nutrient and TSS levels in the lake should be maintained at or below the thresholds (TN < 1.5 mg/L; TP < 0.1 mg/L; N:P ratios between 15 and 20; and TSS < 60 mg/L). These findings can help improve water quality management practices to restore aquatic ecosystems.