Due to their specific effect on photosynthesis, herbicides pose a potential threat to coastal and estuarine microalgae. However, comprehensive understanding of the hazard and risk of these contaminants is currently lacking. Therefore the aim of the present study was to investigate the toxic effects of four ubiquitous herbicides (atrazine, diuron, Irgarol®1051 and isoproturon) and herbicide mixtures on marine microalgae. Using a Pulse Amplitude Modulation (PAM) fluorometry based bioassay we demonstrated a clear species and herbicide specific toxicity and showed that the current environmental legislation does not protect algae sufficiently against diuron and isoproturon. Although a low actual risk of herbicides in the field was demonstrated, monitoring data revealed that concentrations occasionally reach potential effect levels. Hence it cannot be excluded that herbicides contribute to observed changes in phytoplankton species composition in coastal waters, but this is likely to occur only occasionally. Display omitted •The hazard of herbicides for microalgae is compound and species specific.•In general a low risk although occasional potential effect levels are reached.•Current legislation does not protect marine microalgae sufficiently. The hazard of herbicides in the coastal waters is compound and species specific and although the general risk in the field is low, occasionally potential effect levels are reached.