Herbicides have been increasingly used worldwide and a large amount of herbicide residue eventually enters the ocean via groundwater or surface run-off every year. However, the global coastal pollution status of herbicides and their negative impact on marine life (especially phytoplankton) in natural environmental concentrations are poorly understood except for few special environments (e.g. the Great Barrier Reef, Australia). Our field investigation of the distribution of ten triazine herbicides in the Bohai Sea and the Yellow Sea of China revealed that the concentrations of triazine herbicides exceeded the "No Observed Effect Concentrations" for phytoplankton. Their total concentrations could be as high as 6.61 nmol L. Based on the concentration addition model, the toxicity of herbicide homologues is usually cumulative, and the combined toxicity of these ten triazine herbicides could cause 13.2% inhibition on the chlorophyll a fluorescence intensity of a representative diatom species Phaeodactylum tricornutum Pt-1, which corresponds roughly to the toxicity of atrazine in an equivalent concentration of 14.08 nmol L. Atrazine in this equivalent-effect concentration could greatly inhibit the growth of cells, the maximum quantum efficiency of photosystem II (Fv/Fm), and nutrient absorption of Phaeodactylum tricornutum Pt-1. Transcriptome analysis revealed that multiple metabolic pathways (Calvin cycle, tricarboxylic acid (TCA) cycle, glycolysis/gluconeogenesis, etc.) related with photosynthesis and carbon metabolism were greatly disturbed, which might ultimately influence the primary productivity of coastal waters. Moreover, with the values of its bioaccumulation factor ranging from 69.6 to 118.9, atrazine was found to be accumulated in algal cells, which indicates that herbicide pollution might eventually affect the marine food web and even threaten the seafood safety of human beings.