Biomass irregularities in the plankton size spectra of two subtropical shallow lakes have been quantified assuming the classical observed generalities of the size spectra. During a seasonal cycle, three main functional size ranges determined the allocation of the spectra irregularities: microbial food web, nanoplanktonmicroplankton autotrophs, and herbivorous organisms. The structural adjustments within these trophic positions responded to the internal competition between functional guilds, mainly as the result of size-based characteristics related to the ability to eat and the susceptibility to be eaten. Despite the existence of a typical spectrum undulation resulting from self-organization (well-defined trophic positions, limneticbenthic interaction), the biomass irregularities were an indicator of the main interactions disturbing the steady state. The mechanisms responsible for the irregularities operated jointly at ecosystem and individual levels. Thus, the irregular spectra of the eutrophic Laguna Iberá suggested a strong top-down control through cascade effects. Specific properties of peculiar organisms like filamentous cyanobacteria contributed to hold these stable irregularities. The higher spectrum regularity of the meso-oligotrophic Laguna Galarza emerged from a more balanced flow of biomass along the food chain.