The food web efficiency in two contrasting food webs, one phytoplankton based and one bacteria based, was studied in a mesocosm experiment using seawater from the northern Baltic Sea. Organisms included in the experiment were bacteria, phytoplankton, protozoa, and mesozooplankton (copepods). A phytoplankton-based food web was generated by incubating at a high light level with the addition of nitrogen and phosphorus (NP). A bacteria-based food web was created by adding carbon, nitrogen, and phosphorus (CNP) and incubating at a lower light level. In the CNP treatment bacteria dominated the productivity (91%), while in the NP treatment phytoplankton were dominant producers (74%). The phytoplankton community in the NP treatment was dominated by autotrophic nanoflagellates. The food web efficiency, defined as mesozooplankton productivity per basal productivity (phytoplankton + bacteria), was 22% in the phytoplankton-based food web and 2% in the bacteria-based food web. This discrepancy could be explained by 1-2 extra trophic levels in the bacteria-based food web where carbon passed through flagellates and ciliates before reaching mesozooplankton, while in the phytoplankton-based food web there was a direct pathway from phytoplankton to mesozooplankton. The results were supported by stable isotope analysis of mesozooplankton. We propose that climate change, with increased precipitation and river runoff in the Baltic Sea, might favor a bacteria-based food web and thereby reduce pelagic productivity at higher trophic levels.