Waterborne disease threatens public health globally. Previous studies mainly consider that the birth of pathogens in water sources arises solely by the shedding of infected individuals. However, for free-living pathogens, intrinsic growth without the presence of hosts in environment could be possible. In this paper, a stochastic waterborne disease model with a logistic growth of pathogens is investigated. We obtain the sufficient conditions for the extinction of disease and also the existence and uniqueness of an ergodic stationary distribution if the threshold [Formula: see text]. By solving the Fokker–Planck equation, an exact expression of probability density function near the quasi-endemic equilibrium is obtained. Results suggest that the intrinsic growth in bacteria population induces a large reproduction number to determine the disease dynamics. Finally, theoretical results are validated by numerical examples.