Similar to pesticides, genetically modified (GM) GM crops are regulated worldwide and environmental risk assessment is one requirement for environmental release. As a surrogate for aquatic species, non-target tests of GM crops often include Daphnia magna. Developing suitable test protocols for GM plants and D. magna has been challenging, because plant material needs to be ingested by the test organisms (oral mode of action). We here present laboratory studies with insect-resistent GM maize producing multiple Cry proteins from the bacterium Bacillus thuringiensis. Our experiments address several difficulties with such studies, including the suitability of crop plant material as food for D. magna, the separation of Bt protein-effects from plant background effects, and the interpretation of effects in the context of biological relevance and natural range of variation. Daphnia magna can survive, grow and reproduce when fed only maize materials, although the performance was poorer than when fed algae, which indicates nutritional stress. Adverse effects were observed for Bt maize flour, originating from different production fields and years, but not for leaves or pollen, produced from plants grown concurrently in the glasshouse. Because leaves contained eight to ten times more Cry protein than flour, the effects of the flour were probably not caused by the Cry proteins, but by compositional differences between the plant backgrounds. Larger differences in life table and population parameters of D. magna were observed among 5 different non-GM maize lines, which were tested in a similar way to obtain a natural range of variation for each parameter. The protocols established for testing GM crops on D. magna could also be adapted for other orally active substances including, e.g., systemic or RNAi-based pesticides.