An understanding of ongoing changes in biogeochemistry of carbon (C) as influenced by increasing atmospheric deposition (AD) of nutrients is important for integrated water resource management and for exploring options for balancing C sink and fluxes. To determine whether AD-nutrients would increase phytoplankton production and catchment carbon flushing in lakes, we analyzed NO 3 , NH 4 and PO 3 4 in atmospheric deposits, microbial biomass and activity in catchment, nutrient and dissolved organic carbon (DOC) in runoff and, phytoplankton production and sediment-C in six freshwater lakes from 1999 to 2008. Although N: P stoichiometry of AD did not change over time, there was over 1.5 fold increase in AD-NO 3 , NH 4 and PO 3 4 overtime. Microbial biomass and activity in catchments and, DOC and nutrients in runoff increased consistently over time. Lake nutrients, DOC, gross primary productivity, chlorophyll a biomass and sediment-C also showed positive relationship with AD-nutrients. The study indicates that rising input of AD-nutrients steer freshwater lakes towards greater productivity, whereas such inputs in catchment enhance microbial processes and consequently runoff DOC flush and the-coupled effects of these may cause long-term shift in water quality and C balance of these ecosystems.