With the ever-increasing application of carbon dots (CDs), a substantial amount will be released and assemble in the aquatic environment. Nevertheless, potential photodegradation of CDs in the aquatic environment, their accumulation and impacts in aquatic organisms remain unclear. Our study examined the toxicity of CDs to two marine dinoflagellates Prorocentrum micans and Prorocentrum donghaiense. Their bioaccumulation including the uptake and elimination kinetics was also determined. Significant photodegradation of CDs in seawater was observed. Moreover, both the degraded CDs and their photodegradation products were toxic to the dinoflagellates. Although P. donghaiense was more sensitive to CDs than P. micans with the median effect concentration 17.0 and 99.0 mg L⁻¹, respectively, such sensitivity difference disappeared when the toxicity data were plotted against cellularly accumulated CDs instead of their concentration in the experimental medium. Therefore, the higher sensitivity of P. donghaiense was attributable to its higher accumulation of CDs. Overall, the photodegradation and bioaccumulation of CDs should be considered when evaluating their environmental risks.