Herbicide concentrations fluctuate in rivers following crop application and can reach high levels after rain events, yet the duration of these pulses is short. In the present study, we assessed the effect of atrazine and isoproturon pulse exposure on Scenedesmus vacuolatus (Chlorophyceae; strain 211–8b, Kessler) as well as the recovery in the postexposure period. We further explored whether the time-dependent toxicity is similar for herbicides inhibiting the photosystem II (PSII). The growth rate was assessed for different exposure durations, and in addition the inhibition of the effective quantum yield of PSII was measured to monitor the response at the target site. Atrazine and isoproturon did not have similar time-dependent effects on growth rate, despite their same primary mode of action on PSII. Atrazine was less toxic than isoproturon after 10 h of exposure, but the toxicity of both herbicides was similar after 48 h of exposure. However, both compounds inhibited the PSII effective quantum yield within 1 h following exposure. Similarly, the effective quantum yield recovered completely within 4 h after removal of the toxicants, leading to rapid recovery of algal growth. The rapid onset of effects of isoproturon on the growth of the alga during exposure suggests that a single pulse to this herbicide is likely to induce greater effects than an atrazine pulse at the same concentration, even if these effects are reversible. The information gained in the present study should support the effect assessment of sequential exposures as well as the risk evaluation of fluctuating herbicidal exposure.