Changes in rainfall patterns driven by climate change affect the transport of dissolved organic matter (DOM) and nutrients through runoff to freshwater systems. This presents challenges for drinking water providers. DOM, which is a heterogeneous mix of organic molecules, serves as a critical precursor for disinfection by-products (DBPs) which are associated with adverse health effects. Predicting DBP formation is complex due to changes in DOM concentration and composition in source waters, intensified by altered rainfall frequency and intensity. We employed a novel mesocosm approach to investigate the response of DBP precursors to variability in DOM composition and inorganic nutrients, such as nitrogen and phosphorus, export to lakes. Three distinct pulse event scenarios, mimicking extreme, intermittent, and continuous runoff were studied. Simultaneous experiments were conducted at two boreal lakes with distinct DOM composition, as reflected in their color (brown and clear lakes), and bromide content, using standardized methods. Results showed primarily site-specific changes in DBP precursors, some heavily influenced by runoff variability. Intermittent and daily pulse events in the clear-water mesocosms exhibited higher haloacetonitriles (HANs) formation potential linked to freshly produced protein-like DOM enhanced by light availability. In contrast, trihalomethanes (THMs), associated with humic-like DOM, showed no significant differences between pulse events in the brown-water mesocosms. Elevated bromide concentration in the clear mesocosms critically influenced THMs speciation and concentrations. These findings contribute to understanding how changing precipitation patterns impact the dynamics of DBP formation, thereby offering insights for monitoring the mobilization and alterations of DBP precursors within catchment areas and lake ecosystems. © 2024 The Author(s)