This dataset was collected from a mesocosm experiment that focused on how filamentous cyanobacteria alter zooplankton quality and pelagic food web efficiency in the Baltic Sea. The mesocosm experiment was carried out over 29 days using 12 double-mantled high-density polyethylene (HDPE) indoor mesocosm tanks (5 × 0.74 m in diameter) located at the Umeå Marine Sciences Center (UMSC) in Sweden. The experiment consisted of two phytoplankton-based food webs (diatom vs. cyanobacteria (Aphanizomenon)) and two mixing regimes (fast vs. slow) applied in a 2×2 factorial design. During the experiment, we collected samples once a week for phytoplankton and mesozooplankton counting, heterotrophic bacterial production, primary production, and stable isotopes (13C and 15N) of seston. At the end of the sampling period, we collected sedimentation and mesozooplankton samples for stable isotope and fatty acid analysis. Mesozooplankton and seston samples were also collected for thiamin analyses at the beginning and end of the sampling period. The sampling strategy for various parameters is indicated in Table 1. Each tab in the Excel file contains data on various measurements collected at different time periods.