© 2020, Springer Science+Business Media, LLC, part of Springer Nature.Human-induced changes in external nutrient loading affect the phytoplankton community and abundance directly by changing the amount of nutrients available, but also indirectly through changes in the zooplankton (that is, grazer) community structure, mediated in part by changes in the fish community structure and biomass. Such shifts affect the species dynamics and community succession of lake phytoplankton communities, and they may ultimately influence community stability. However, the relative importance of different biotic mechanisms influencing the community stability of phytoplankton along nutrient and associated zooplankton grazing pressure gradients remains unclear. Here, we evaluated the importance of four potential stabilizing biotic metrics—taxon richness, synchrony, community dominance and biomass of phytoplankton to the seasonal stability over two decades of re-oligotrophication in 20 Danish lakes. We found no clear temporal patterns in seasonal stability across lakes but considerable variations in the individual lakes. Total phosphorus (TP) affected the seasonal stability of the phytoplankton communities either directly or indirectly through changes in community dominance. Total nitrogen (TN) influenced the seasonal stability indirectly via changes in phytoplankton taxon richness, synchrony, and community dominance. Grazer richness (that is, zooplankton taxa richness) impacted the seasonal stability indirectly through changes in phytoplankton taxon richness and synchrony. Grazing pressure, using the biomass ratio of zooplankton:phytoplankton as a proxy, had an indirect effect on seasonal stability via changes in synchrony and community dominance. Compensatory dynamics (as indicated by the synchrony of phytoplankton) exerted dominant control of phytoplankton seasonal stability at high TN and high grazer richness and pressure, while the portfolio effect (as indicated by taxon richness) contributed to phytoplankton seasonal stability at low TN and high grazer richness. However, a strongly negative selection effect (as indicated by community dominance of phytoplankton) was observed at high nutrient levels and low grazer richness. Grazer richness and grazing pressure had stronger stabilizing effects on the seasonal succession of the phytoplankton communities than did TP and TN. Our results highlight how various biotic mechanisms (for example, compensatory dynamics and portfolio effect) can change in their importance in maintaining the seasonal stability of phytoplankton communities subjected to nutrient and grazer control.