Bacteria are important components of lake ecosystems, playing a crucial role in driving the cycling of elements and regulating water quality in lakes. Uncovering the mechanisms underlying the formation and maintenance of bacterial community diversity in lakes, known as community assembly mechanisms, is a central objective in the study of microbial ecology in lakes. In recent years, the development of microbiomics has greatly promoted the understanding of the assembly mechanisms of bacterial communities in lakes. Eutrophication represents one of the most important environmental challenges faced by lake ecosystems in China today, and it is also a nonnegligible factor determining the composition and diversity of bacterial communities in lakes. This article firstly provides a review of the theoretical foundations and the developmental context of bacterial community assembly mechanisms in lakes. Secondly, it outlines the main analytical methods used in studying the assembly mechanisms of bacterial communities in lakes. Next, it summarizes the latest research advancements in understanding the impact of eutrophication on the assembly mechanisms of bacterial communities in lakes. Finally, it discusses future research prospects and the challenges faced in studying the assembly mechanisms of bacterial communities in lakes under the influence of eutrophication.