Genetically modified organisms are used extensively in agriculture. To assess potential side effects of genetically modified (GM) plant material on aquatic ecosystems, only a very small number of higher-tier studies have been performed. At the same time, these studies are particularly important for comprehensive risk assessment covering complex ecological relationships. Here we evaluate the methods of experimental higher-tier effect studies with GM plant material (or Bt toxin) in comparison to those well-established for pesticides. A major difference is that nominal test concentrations and thus dose-response relationships cannot easily be produced with GM plant material. Another important difference, particularly to non-systemic pesticides, is that aquatic organisms are exposed to GM plant material primarily through their feed. These and further differences in test requirements, compared with pesticides, call for a standardisation for GM-specific higher-tier study designs to assess their potentially complex effects in the aquatic ecosystems comprehensively.