We tested the sensitivity of nine submersed macrophyte species to the fungicides chlorothalonil, pentachlorophenol, fluazinam, and carbendazim. Endpoints determined 3 weeks after the start of the treatment were based on shoot and root growth in water. Carbendazim proved not or only moderately toxic to these macrophytes. Pentachlorophenol and chlorothalonil were more toxic than fluazinam. Taking all endpoints into consideration, toxicity levels differed very substantially. Although root endpoints reflecting root growth were in some cases more sensitive than shoot endpoints, shoot growth endpoints like relative growth turned out to be more reliable than the root growth endpoints. Due to the large differences in the type of mode of action between fungicides, it is very difficult to predict their potential effect in the environment or even to predict whether non-target organisms like macrophytes are likely to be sensitive. Ideally, therefore, the registration of fungicides requires an extensive risk-assessment procedure, which also covers non-target groups like macrophytes.