Lake ecosystems are critical slow-flow environments where silver nanoparticles (AgNPs) and bacterio-plankton interact. AgNPs, known for their strong antimicrobial activity and unique physicochemical properties, are widely used across industries but raise environmental concerns due to their size-depen dent distinct biochemical effects. Dissolved organic matter (DOM), primarily shaped by microbial activity, constitutes a key organic carbon component in lakes. Understanding DOM turnover under the influence of AgNPs is essential for gaining deeper insights into carbon cycling within lake ecosystems. This study investigated the effects of AgNPs on DOM properties using advanced spectroscopic techniques, highlighting the size-dependent impacts on bacterial community structures and DOM characteristics. Smaller AgNPs exhibited greater microbial toxicity, leading to higher concentrations of protein-associated C1 components within DOM. Furthermore, DOM influenced the transformation of silver between ionic and nanoparticle forms, modulating the toxicity of silver species. AgNPs also enhanced associations between specific bacterial taxa and environmental indicators. Size-dependent effects of AgNPs substantially altered microbial functions related to carbon and nitrogen cycling, affecting bacterial metabolism and the environmental behavior of functional genes. These findings underscore the pivotal role of nanomaterial size in shaping DOM turnover, bacterial community interactions, and biogeochemical processes. Overall, this study provides a foundational understanding of the ecological implications of AgNPs in lake ecosystems and informs future environmental risk assessments.