We conducted comprehensive field investigations to characterise the trophic status and food web structure of Großer Vätersee (GV) and Kleiner Vätersee (KV), two stratified lakes in the Baltic lake region of northeastern Germany. The lakes will be used as manipulation (GV) and reference (KV) ecosystems in food web studies. Both lakes are mesotrophic to slightly eutrophic with mean epilimnetic total phosphorus (P) concentrations of 24 and 21µg L-1 in GV and KV, respectively. Mean phytoplankton biomass was 0.9 and 0.5 cm3 m-3 in GV and KV. During summer, the algal community of both lakes was dominated by cyanobacterial picoplankton and Ceratium spp. Filamentous cyanobacteria (mostly Planktothrix sp.) prevailed in a deep chlorophyll maximum found within the chemocline of both lakes. Bacterial biomass in the epilimnion of GV usually ranged between 1 and 3 cm3 m-3. Mean ciliate abundance was 13 ind. mL -1 in GV and 14 ind. mL-1 in KV. While Oligotricha dominated in GV, Scuticociliata were found most frequently in KV. Mean annual crustacean biomass was high in both lakes (GV 2.5 cm3 m-3, KV 1.2 cm3 m-3); Eudiaptomus gracilis, E. graciloides and Daphnia spp. were the most prominent species. Total fish biomass of both lakes was dominated by roach (GV 52 %; KV 57 %) and perch (GV 24 %; KV 34 %) Vaucheria dichotoma and Chara spp. dominated the macrophyte community in GV; Chara spp. dominated in KV. The slightly higher trophic status of GV was most likely a result of greater P accumulation in the sediments due to external loading, which resulted in greater hypolimnetic P concentrations throughout the summer in GV. However, on an annual basis these differences were only occasionally reflected at higher trophic levels. The differences in fish biomass, however, might have been a consequence of higher structural diversity in GV provided by submersed macrophytes rather than its higher trophic status. We conclude that the trophic characteristics and food web structure of Großer Vätersee and Kleiner Vätersee are similar enough to be suitable as manipulation and reference lakes in food web experiments.