The effects of toxin producing plankton and environmental stochasticity are intriguing problems in marine plankton ecology. To observe the effect of stochastic fluctuation, a non-toxic phytoplankton, toxic phytoplankton and zooplankton (NTP-TPP-Z) system with an assumption that the grazing pressure of zooplankton decreases due to toxic phytoplankton is proposed and analysed. The nature of the dynamics of the system is observed for both the deterministic model and the model with stochastic perturbation around the positive equilibrium. Exchange of stability is also observed for both the cases. To validate the analytical results, numerical experiments and field collected sample observations are also presented. We conclude that the deterministic extinction may be controlled by monitoring the intensity of white noise or artificial eutrophication. Copyright © 2003 John Wiley & Sons, Ltd.