Previous studies reported adverse effects of genetically engineered maize that produces insecticidal Cry proteins from Bacillus thuringiensis (Bt) on the water flea Daphnia magna. In the current study, effects of flour, leaves, or pollen from stacked Bt maize that contains six Bt proteins (SmartStax) in two plant backgrounds on life table parameters of D. magna were investigated. 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 a 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. Furthermore, considering the natural range of variation in the response of D. magna to conventional maize lines, the observed effects of Bt maize flour were unlikely to be of biological relevance. Our study demonstrates how Cry protein effects can be separated from plant background effects in non-target studies using Bt plant material as the test substance and how detected effects can be judged for their biological relevance.