In this paper, we present a stochastic eutrophication-chemostat model with impulsive dredging and pulse inputting on environmental toxicant. The sufficient condition for the extinction of microorganisms is obtained. The sufficient condition for the investigated system with unique ergodic stationary distribution is also obtained. The results show that the stochastic noise, impulsive dredging, and pulse input on the environmental toxicant play important roles in the extinction of microorganisms. The results also indicate the effective and reliable controlling strategy for water resource management. Finally, numerical simulations are employed to illustrate our results.