Monitoring (1997-2012) was focused on the impact of gray forest soils (Luvic Greyzemic Phaeozems) pollution with aluminum industry fluorides on carbon transformation and agroecosystems functioning at the background of present day climatic changes. Air temperature increase compared to «climatic norm» (1961-1990) was found to closely correlate with СО2 emission, but not to affect soil microbe biomass carbon content (Cmic). Systemic analysis of carbon transformation consequences demonstrated negative influence of fluorides on carbon flow integrated agroecosystem components (soil-microorganisms-plants-atmosphere), particularly in anomalous years. The regimes of agroecosystems functioning and its environmental loads were evaluated by the proportion of flows of net-mineralized and (re)immobilized (N-M:RI) carbon.