<p>Bacterial growth efficiency (BGE), defined by the balance between bacterial production (BP) and respiration (BR), is a key indicator of microbial metabolism and carbon fluxes in freshwater ecosystems. Although bottom-up controls on BGE are well recognized, the relative importance of top-down processes, particularly viral lysis and grazing, remains poorly understood. To evaluate the influence of mortality pathways on bacterially mediated carbon fluxes, we conducted a seasonal time-series study in Lake Cournon, sampling both the euphotic zone and bottom waters. BGE exhibited marked seasonal variability (14–53%) that exceeded depth-related differences, reflecting shifts in the balance between BP and BR associated with bacterial biosynthesis and carbon mineralisation. No significant relationships were observed between BGE and bottom-up controls, suggesting a stronger role for mortality-driven processes. Viruses negatively affected BGE, likely through preferential lysis of highly active high-nucleic-acid bacterial populations that contributed substantially to bacterial productivity. Viral lysis appeared to stimulate BR more than BP in the remaining bacterial community through the release of dissolved organic matter, resulting in lower BGE at the community level. In contrast, size-selective grazing by nanoflagellates exerted a positive influence on BGE, likely by recycling nutrients and stimulating the growth of active bacterial populations. Overall, our findings demonstrate that the mode of bacterial mortality can strongly regulate bacterial carbon metabolism and alter the pathways of organic carbon flow in freshwater ecosystems.</p>