In this article, the complex relationship between phytoplankton and zooplankton with a particular emphasis on the effects of toxins produced by phytoplankton and the environment on their population dynamics is investigated. It is presumed that the environmental toxin impacts phytoplankton growth which follows the logistic growth. A Holling type II functional response is used to explain how zooplankton preys on phytoplankton and how toxins are transferred between them. The model incorporates a linear technique for both species’ harvesting. A thorough investigation is conducted on important aspects of the system, including stability at different equilibrium points, boundedness, and positivity. Furthermore, the possibility of transcritical and Hopf bifurcations at various equilibria is investigated. Numerical simulations demonstrate how phytoplankton harvesting and toxin release, along with species coexistence and system stability, influence plankton blooms. The study identifies crucial thresholds for maintaining species coexistence and controlling plankton blooms.