Microbial community assembly is shaped by deterministic and stochastic processes, but the relationship between these processes and the environment is not understood. Here we describe a rule for the determinism and stochasticity of microbial community assembly affected by the environment using in silico, in situ, and ex situ experiments. The in silico experiment with a simple mathematical model showed that the existence of essential symbiotic microorganisms caused stochastic microbial community assembly, unless the community was exposed to a non-adapted nutritional concentration. Then, a deterministic assembly occurred due to the low number of microorganisms adapted to the environment. In the in situ experiment in the middle of a river, the microbial community composition was relatively deterministic after the drastic environmental change caused by the treated wastewater contamination, as analyzed by 16S rRNA gene sequencing. Furthermore, by culturing microbial communities collected from the upstream natural area and downstream urban area of the river in test tubes with varying carbon source concentrations, the upstream community assembly became deterministic with high carbon concentrations while the downstream community assembly became deterministic with low carbon concentrations. These results suggest that large environmental changes, which are different from the original environment, result in a deterministic microbial community assembly.