<p>Benthic macroinvertebrates play a critical role in regulating microbial processes in lake sediments; however, their taxon-specific effects on sedimentary bacterial production (BP) remain poorly understood. This study experimentally examines the influence of three crustacean taxa, <i>Jesogammarus annandalei</i> (Amphipoda), <i>Asellus hilgendorfii</i> (Isopoda), and <i>Palaemon paucidens</i> (Decapoda), and one oligochaete species (<i>Tubifex tubifex</i>) on BP in the profundal sediments of Lake Biwa, Japan. Intact sediment cores were collected and incubated under controlled conditions, with or without the addition of macroinvertebrates. BP was quantified using a stable isotope method based on ¹⁵N-labeled deoxyadenosine. Crustacean additions significantly increased BP compared to the controls, likely through bioturbation and nutrient excretion, while <i>T. tubifex</i> significantly suppressed BP, presumably due to grazing by <i>T. tubifex</i> on the bacteria. Linear regression analysis revealed that BP was positively correlated with sediment organic content (ignition loss) in most treatments, but not in the <i>A. hilgendorfii</i> treatment, suggesting complex species-specific interactions. Interestingly, <i>A. hilgendorfii</i> was also associated with a significant increase in ignition loss, potentially due to sediment mixing. Our results highlight the taxon-specific functions of benthic macroinvertebrates, suggesting that shifts in community composition may substantially affect microbial processes and sediment ecosystem functions in deep-lake environments.</p>