Dissolved oxygen (DO) concentrations in euphotic waters are governed by the combined effects of air-sea exchange, photosynthesis, and aerobic respiration. Bacteria and microeukaryotes both respond to, and help shape, these oxygen dynamics, yet the quantitative contributions of microbial traits versus physicochemical factors to DO variability remain poorly understood. Moreover, the extent to which DO, and other environmental parameters or inter-domain biotic interactions control microbial diversity and abundance is still unresolved. To fill these gaps, we conducted a two-month summer survey of a shallow coastal area off Shandong Peninsula, a region frequently affected by seasonal hypoxia. A stepwise regression model parameterizing environmental variables and a range of mi-crobial factors indicated that environmental factors (principally dissolved silicate and pH) explained the majority of DO variance in surface and bottom waters, whereas at mid-depth a suite of microbial factors (most notably the abundance of high nucleic acid bacteria) collectively outperformed physicochemical variables in explanatory power. Under hypoxic conditions, microbial abun-dances declined and community structures of bacterioplankton and pico-nanoeukaryotes shifted significantly, yet alpha diversity metrics remained unchanged. Further analyses indicated that abundance, diversity and community structure of bacterioplankton were governed primarily by interactions with pico-nanoeukaryotes, whereas these of pico-nanoeukaryotes were influenced to comparable degrees by environmental and biotic factors. Overall, bottom-water deoxygenation in this coastal system is predomi-nantly by physiochemical processes, especially nutrients loading and stratification, rather than by direct microbial feedback. Non-DO environmental variables and inter-domain interactions emerge as the principal forces structuring planktonic communities, under-scoring the need for nutrient-management strategies that account for these complex biotic-abiotic linkages.