Abstract Submerged aquatic macrophytes are important in shallow aquatic ecosystems because they stabilize the macrophyte-dominated state by increasing water transparency in various ways. One of these is the excretion of allelopathic substances inhibitory to phytoplankton, but it is still controversial whether this mechanism can be important in the field. We developed a model that describes phytoplankton growth including the effects of two different macrophytes (Chara sp. and Stratiotes aloides), which ar Both macrophyte species had a considerable effect on phosphorus levels in the water. Shading of phytoplankton by Chara sp. was estimated to be negligible. This macrophyte species has a growth form close to the sediment. The allelopathic activity of Chara sp. caused a phytoplankton growth reduction of ca. 5–10%, while the most pronounced effect seems to be related to reduction of resuspension. S. aloides floats on the water surface during spring and summer. Therefore, it has a potentially high shading effect. Additionally, this species has a relatively strong allelopathic capacity, sometimes resulting in a reduction of phytoplankton between 50 and 80%. The model suggests that the relative contribution of allelopathy in situ is low or negligible for charophytes. Only for macrophyte species that have a high allelopathic potential, like S. aloides, it may be a significant effect.