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Heterotrophic marine bacteria are key players in the ocean carbon cycle. However, their exact contributions to net community production (NCP)—a crucial metric for the biological pump that indicates the metabolic balance and sets the upper limit for carbon export—remain unquantified due to limited bacterial integration in ocean biogeochemical models. In this study, we addressed this knowledge gap and quantified the role of bacterial dynamics in controlling total heterotrophic respiration (HR) and NCP at the Bermuda Atlantic Time‐series Study (BATS) site. To do this, we developed and employed a one‐dimensional data‐assimilative ocean biogeochemical model. Our results demonstrated that bacteria contributed 88% of HR, playing a dominant role in regulating NCP through respiration rates comparable to net primary production (NPP). Under future climate conditions, annual NCP remained stable in the upper ocean due to offsetting increases in bacterial respiration (BR) and NPP. However, distinct seasonal and vertical patterns emerged that intensified with the severity of climate change: increased NCP in winter and early spring surface waters, decreased NCP in late spring and at depth during mixing periods, and less pronounced increases during summer‐fall stratification. The increased BR rates resulted from complex interactions between temperature‐enhanced metabolic rates and adaptive substrate utilization, where bacteria maintained their metabolism despite increased labile organic matter limitation by utilizing a semi‐labile pool. Our results highlight bacteria's critical influence on upper ocean carbon cycling, providing key insights into their biogeochemical role under climate change.