Standing dissolved oxygen (DO) in euphotic waters is largely a net balance of primary production of phytoplankton, aerobic respiration of heterotrophs, and exchange between atmosphere and sea surface. Previous microbial studies often focus on how hypoxia affect microbial diversity. In this study, we explored how microbial diversity and structure of both bacterial and eukaryotic microbes, together with environmental factors, related to the variation of DO level, and the occurrence of hypoxia in a coastal ranch. Based on a stepwise regression model, we found that integrating microbial traits of their communities (e.g., cell abundance, alpha diversity and relative abundances of major groups) and environmental factors did enhance the explanatory power for the DO variation across surface, middle and bottom water layers, with an increase of 38% for the middle layer. We also observed significant differences in the relative proportions of the main lineages of bacterioplankton and pico-nanoeukaryotes at different DO levels. Under hypoxic conditions, the proportion of certain low-oxygen-tolerant microbial groups increased, while under normal oxygen concentration conditions, an increase in photosynthetic microbial groups was observed.