Detecting allelopathic inhibition of phytoplankton by submerged macrophytes in an ecologically meaningful way is not easy. Multiple-approach investigations from a laboratory scale to the ecosystem level have been recommended to overcome the shortcomings of individual methods. Whether results of different methods are qualitatively or quantitatively comparable has not yet been tested. Here, we compare the sensitivity of the green algae Desmodesmus subspicatus (Chodat) E. Hegewald et Ant. Schmidt and Stigeoclonium helveticum Vischer to the allelopathic effect of the submerged macrophyte Myriophyllum verticillatum L. The following three approaches were used: (i) coincubation of algae in dialysis membrane tubes in a lake inside and outside a M. verticillatum stand, (ii) coincubation of algae in dialysis membrane tubes in aquaria with and without M. verticillatum, and (iii) single additions of tannic acid (TA), an allelopathically active polyphenol present in this macrophyte, to the algae cultures. For each method, fluorescence-based (chl a, PSII activity) and particle-based (cell count, biovolume) parameters were compared after 48 h of incubation. Results revealed quantitative and qualitative differences between methods. Algae incubated in dialysis membrane tubes in aquaria showed a strong decrease in all parameters under the influence of macrophytes. In situ measurements were influenced by adverse growth conditions for the test algae and only detected significant reductions for biovolume. Single additions of TA induced a strong reduction of fluorescence-based parameters similar to aquarium results, but an increase in the cell count. Even the qualitative transfer of laboratory results to field conditions thus requires caution and a proper selection of parameters.