Abstract: Nanoplastics (NPs) and herbicide prometryn are common pollutants in the marine environments, but their joint impacts on marine microalgae is unclear. In this study, we investigated the toxic effects of environmental concentrations of prometryn (500 ng/L) and polystyrene nanoplastics (70 nm, 20, 200, and 2000 μg/L) on Cyclotella cryptica. The results showed that 20, 200 and 2000 μg/L NPs significantly reduced photosynthetic pigment content, damaged algal cell structure, and hindered the population growth of C. cryptica. Whereas 500 ng/L prometryn had no significant effect on the early growth of C. cryptica. In the presence of environmental concentrations of prometryn, NPs-induced growth inhibition was significantly enhanced, especially after 24 h of exposure; algal density in the prometryn and 2000 μg/L NPs combined exposure groups was reduced by 19.4% compared with that of the 2000 μg/L NPs single exposure group. Moreover, the environmental concentrations of prometryn aggravated the damage of NPs to the algal cells, which increased the membrane permeability to 1.6 times that of the control group (P < 0.05). Damage to the cell membrane reduced the ability of algal cells to resist the NPs and thus exacerbated the toxicity of NPs to C. cryptica. Compared to the 2000 μg/L NPs single exposure, the combined exposure of prometryn and 2000 μg/L NPs increased the mortality and proportion of anomalous cells by 4.1% and 3.4%, respectively. The results of this study provide a reference for assessing the hazards of NPs and herbicide pollution on marine primary productivity.