In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes multiple layers of stochasticity, from small Brownian fluctuations, to possibly large changes due to environmental `shifts'. We are able to give a full classification of the asymptotic behavior of these models. New techniques had to be developed to prove the persistence and extinction of the process as the system is not in Kolmogorov form and, as a result, the analysis is significantly more involved.