The majority of ecotoxicological enclosure experiments monitor species abundances at different chemical concentrations. Here, we present a new modelling approach that estimates changes in food web flows from such data and show that population- and food web level effects are revealed that are not apparent from abundance data alone. For the case of cypermethrin in freshwater enclosures, photosynthesis and excretion (d−1) of phytoplankton at 3.643 μg L−1 cypermethrin were 30% lower and 100% higher than in the control, respectively. The ingestion rate of mesozooplankton (d−1) was 6 times higher in the treated enclosures than in the control as food concentration increased with insecticide exposure. With increasing cypermethrin concentrations, nanoflagellates progressively relied on phytoplankton as their main food source, which rendered the food web less stable. We conclude that this tool has excellent potential to analyse the wealth of enclosure data as it only needs species abundance and general constraints. Food web modelling infers population- and food web level effects of chemicals from species abundance.