1. Phytoplankton dynamics, food chain changes and resilience in Lake Zwemlust, a shallow lake in The Netherlands, are described for the period 1986–94.2. After biomanipulation in 1987, the lake moved through two alternative states, while the external nutrient loadings were maintained. A clear‐water phase, mostly dominated by macrophytes, persisted from 1987 to 1991, and a rather turbid state, dominated by algae, occurred in the summers of 1992–94, after several consecutive and sustained perturbations affecting different parts of the food web in the lake. These two periods were characterized by different community structures.3. The phytoplankton assemblage gradually changed in a pattern that reverted in later years towards that of the pre‐biomanipulation stage, although the same species composition was not regained. This agrees with some mathematical models. During the clear‐water phase, nutrient shortage, light climate and zooplankton feeding selected in favour of small, high surface : volume ratio and rapidly reproducing algae. However, in mid‐summer of 1992–94, nutrient availability and cladoceran grazing on edible algae favoured cyanophytes.4. Nutrients were transferred to higher trophic levels or lost from the system at relatively high rates when the lake was in a piscivore–macrophyte‐dominated state, while they tended to accumulate in the algae in a planktivore‐dominated chain without macrophytes. The role of weed beds was central for nutrient competition (mostly nitrogen) with algae, as well as a refuge and a base for alternative food sources to grazers. Weed beds seemed to have a strong effect in increasing connectedness, resilience and stability of the lake community.5. The complete return of Zwemlust to a turbid state dominated by phytoplankton seems to have depended upon turnover of the limiting nutrient, which was retarded by macrophytes and stimulated by planktivorous fish and waterfowl.