Recent advances in phytoplankton modelling have used species-rich, self-organising assemblages. These models have shown that phytoplankton with complementary life-history traits related to resource exploitation assemble into stable states of lumpy coexistence when resources fluctuate where species niches occur in clusters along resource gradients. They have also shown that a high degree of competitive dissimilarity between clusters arises, and that this relates to the incidence of monospecific blooms of allelochemical-producing taxa, i.e. some harmful algal bloom (HAB) species. These findings further suggest that the mode (sudden v. gradual changes) under which limiting resources fluctuate plays an important role in determining the emergent properties of the assemblage. For example, productivity, biodiversity and the number of species clusters (and, therefore, resistance to HABs) are all enhanced when switches in resource supplies are gradual, compared with when they are sudden. These theoretical findings, as well as others discussed herein, are of particular interest in watersheds where human activities, such as dam construction, have the capacity to dramatically alter natural-resource fluctuation patterns.