Abstract: This study explores the role of benthic macroinvertebrate communities in shaping the composition and dynamics of dissolved organic matter (DOM) at the sediment–water interface in the river-lake confluence zone of Nansi Lake, a transitional area characterized by high ecological complexity. The optical properties of DOM in both water and surface sediment samples were characterized and assessed, using parallel factor analysis (PARAFAC), fluorescence regional integration (FRI), and redundancy analysis (RDA) associated with macroinvertebrate community structure. Results showed that DOM primarily consisted of fulvic acid-like substances, soluble microbial by-products, tryptophan-like, and tyrosine-like substances. The relative abundance and composition of these DOM fractions were closely linked to the distribution and functional traits of dominant macroinvertebrate taxa. Water-column DOM was mainly derived from autochthonous sources, while sediment DOM exhibited higher molecular weight and lower humification levels, suggesting enhanced microbial by-product generation induced by biological disturbance, particularly bioturbation, from benthic fauna. This process also facilitated the upward flux of DOM from sediment to overlying water. RDA results revealed distinct species-specific effects. Gastropod-dominated communities tended to suppress the formation of UV-region fulvic acids and microbial by-products in water, whereas communities dominated by swimming invertebrates (e.g., shrimps, aquatic insects) significantly promoted microbial by-product accumulation in sediments. Species such as Neocaridina denticulata sinensis, Biomphalaria glabrata, and Bellamya purificata were consistently associated with increased microbial by-product fractions, indicating that collector-gatherers and deposit-feeders exert a pronounced influence on DOM transformation pathways. Moreover, DOM composition exerted a feedback effect on benthic community structure. Shifts in protein-like DOM components, for instance, were linked to changes in the abundance of certain taxa, implying a bidirectional interaction between biological activity and organic matter dynamics. Communities with higher functional diversity and complementary feeding strategies facilitated DOM turnover and carbon cycling efficiency, while species-poor communities often exhibited selective consumption or suppression of specific DOM fractions. These findings highlight the critical role of macroinvertebrate communities as both drivers and responders in sediment–water carbon exchange. Their bioturbation and feeding behaviors not only modify DOM composition but also mediate microbial activity and nutrient fluxes at the interface. Importantly, functional group identity and community integrity emerged as key regulators of DOM fate, challenging the assumption of functional redundancy in benthic ecosystems. This study provides new insights into the ecological coupling between biological communities and carbon biogeochemistry in freshwater systems. It underscores the necessity of integrating benthic fauna diversity, functional traits, and biogeochemical processes into DOM modeling and aquatic ecosystem management frameworks.