Warming, eutrophication, and land use changes are all major drivers in increasing lake hypoxia, an important control on carbon cycling in lakes. Culturally meromictic lakes with permanently anoxic monimolimnia are an extreme response to such perturbations. Here we present results from water column and sediment core measurements at Brownie Lake (Minnesota, U.S.A.), which transitioned to meromixis due to basin disturbances in the 1910s, and enhanced stratification due to runoff of road deicing salts since the 1950s. Brownie Lake has some of the highest methane emissions reported for freshwaters with low C:N and depleted δ ¹³C indicating an autochthonous source of particulate organic carbon. Iron is the dominant terminal electron acceptor in the monimolimnion due to the dearth of oxygen, sulfate, and nitrate resulting in ‘ferruginous’ conditions (i.e., abundant dissolved ferrous iron). A reaction-transport model based on data from the water and sediments shows a high efficiency of methanogenesis compared to other modes of organic carbon remineralization, indicating the importance of terminal electron acceptor availability in carbon dynamics of anoxic lakes. The average sediment organic carbon decreased after the onset of meromixis (from 26 wt% to 9 wt%). The average sediment iron increased (from 0.4 wt% to 2.60 wt%) after the onset of ferruginous conditions. Future results will include DNA sequencing and biomarker analysis to determine if there was a coeval shift in microbial community and carbon cycling in the lake during these transitions.