Herbicide-induced phytoplankton inhibition threatens coastal biodiversity and ecosystem function. Although studies employing single-frequence exposure aid in understanding the phytoplankton community's responses to herbicides, it’s difficult to objectively assess their response to cyclic herbicide inputs (long-term low-dose and short-term high-dose) in marine ecosystems. Here, we analyzed the concentration and distribution of herbicides in global coastal waters and simulated this cyclic process through a two-phase atrazine exposure mesocosm experiment and laboratory tests. The results indicated that, the herbicide concentrations (0.82 nmol L−1, 95 % CI 0.55, 1.74) from May to August were significantly higher than that (0.14 nmol L−1, 95 % CI 0.02, 0.38) in the remainder months, and highest concentrations typically emerged in summer; the changes in phytoplankton community composition under environmental concentrations of triazine herbicides could recover in the short term, but sustained inhibition of biomass was produced; the dominant populations were more likely to develop tolerance through preexposure and recover from subsequent impulse of atrazine, but this process was accompanied by the loss of rare groups and a decrease in biodiversity, meanwhile, affected the bacterial community in phycosphere. Consequently, we considered that the cyclic herbicide inputs may cause more detrimental effects than single-frequence exposure, potentially leading to a large-scale decline in coastal primary productivity.