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Cyanobacterial blooms in marine and freshwater ecosystems have increased in magnitude, frequency, and distribution worldwide during recent decades. Filamentous cyanobacteria are of unsuitable size for mesozooplankton feeding and of poorer nutritional quality than other phytoplankton taxa. The production and quality of higher trophic levels are therefore expected to decrease when cyanobacterial blooms increase. We conducted a mesocosm experiment using natural seawater from the northern Baltic Sea to contrast the effects of cyanobacteria- (Aphanizomenon flosaquae) and diatom-dominated phytoplankton communities on mesozooplankton production and nutritional quality. A low and a high hydrological mixing regime was applied. The δ15N isotopic signal of seston and mesozooplankton was lower in the cyanobacteria-based food web, demonstrating that Aphanizomenon fixed atmospheric nitrogen, which was transferred in the food web. The biomass of edible-sized phytoplankton (2–50 μm) was lower in the cyanobacteria-based food web. The fatty acid quality, indicated by the ω3:ω6 ratio, was lower in the cyanobacteria-based food web for both phytoplankton and mesozooplankton. Together, this resulted in 75–80% lower copepod production and food web efficiency (FWE) in the cyanobacteria-based food web than in the diatom-based food web. The hydrological mixing regime did not affect the biological production and quality. The results demonstrate that copepod production and FWE were driven by the quality and production of edible-sized phytoplankton. The study implies that climate-induced increases of filamentous cyanobacterial blooms will cause decreased production and nutritional quality of higher trophic levels.