Many coastal oceans experience not only increased loads of nutrients but also changes in the stoichiometry of nutrient supply. Excess supply of nitrogen and stable or decreased supply of silicon lower silicon to nitrogen (Si:N) ratios. We used a multi-factorial mesocosm experiment to examine how Si:N ratios affect plankton community composition and food web structure in a Baltic Sea plankton community. Our results suggest that declining Si:N ratios favor microzooplankton and mixoplankton leading to increased complexity of planktonic food webs. The associated consequences on higher trophic levels are moderated by edibility, nutritional value or toxicity of dominant phytoplankton species.