<p>Deterministic and stochastic processes are important to the formation of biological communities in community assembly mechanisms. However, the mechanisms of community assembly of phytoplankton and benthic diatoms are still poorly understood in different periods and regions in urban wetlands. In this study, we collected phytoplankton and benthic diatom samples from eight urban wetlands in cold regions from April 2023 to March 2024. We then examined distance–decay relationships (DDRs) patterns across three regions (the Northern Songhua River, Songhua River and Southern Songhua River) and four periods (dry, wet, freezing and frozen seasons). We observed significant DDRs curves in the phytoplankton community among different periods and regions, with the DDRs slopes being found in the Songhua River. Furthermore, variation partition analysis and structural equation modeling revealed that spatial and environmental factors had different effects on phytoplankton and benthic diatom communities. These findings suggest that phytoplankton communities were driven by stochastic process, while the deterministic process was a slightly stronger influencing factor in the assembly of benthic diatom communities. Together, the results of this study provide a scientific basis for the management and protection of water ecosystems in cold regions and help explain microbial diversity in urban wetlands.</p>