Although several studies explain the trophic cascade in water systems, we lack knowledge about top-down–bottom-up effects on phytoplankton from eutrophic lakes. In this study, we tested the importance of trophic cascades on phytoplankton structure, predicting that environmental variations are the main drivers. We performed a monthly sampling during a year to measure environmental variables, phytoplankton and zooplankton, plus two samplings (winter and summer) to assess fish structure. Furthermore, we analyzed zooplanktivorous fish stomach-gut contents and completed a hatching zooplankton resting egg experiment to assess the effect of fish on dormant populations. We ran a partial redundancy analysis (pRDA) for phytoplankton using zooplankton, nutrient availability and environmental variables as predictor variables. We finally calculated several ratios of the zooplankton:phytoplankton biovolume to assess potential predation effects. Phytoplankton was correlated with variations in temperature and conductivity plus nutrients (pRDA: 63.4%, F = 4.6, P = 0.001) and was dominated alternatively by diatoms and cyanobacteria. Zooplankton was dominated by microphagous rotifers (> 45% of the total biovolume), and only the ratio of microphagous rotifer:small chlorophytes was significant during summer and autumn (F = 10.6, P = 0.005). The fish community was dominated by insectivorous-planktivorous fish (> 65% of total density), yet a negative selection of zooplankton items (Ivlev’s index < 0) was found. Nevertheless, the zooplankton resting stage analysis showed that microphagous Rotifera were dominant (29 species emerged), suggesting a structuring effect of fish on the zooplankton size. We conclude that phytoplankton was mainly controlled by environmental variations plus nutrient availability, while top-down had a less evident effect.