Mercury (Hg) is a chemical element widely present in the Earth's crust. However, its high toxicity and ability to accumulate in organisms and biomagnify through food chains characterize it as a global pollutant of primary control. We assessed total mercury concentrations ([THg]) in abiotic and biotic compartments from 98 floodplain lakes associated with the Araguaia River and six tributaries (Midwest Brazil). [THg] quantification in water was performed by cold vapor atomic fluorescence spectroscopy. [THg] in bottom sediment was assessed using cold vapor generation atomic absorption spectrophotometry, while [THg] in macrophyte, periphyton, and plankton were quantified by thermal decomposition atomic absorption spectrometry. Hotspots of [THg] in water, bottom sediment, and macrophytes were determined in areas impacted by pasture and urban areas. In contrast, hotspots of [THg] in periphyton and forest fires were determined in preserved areas downstream. [THg] in plankton did not show a clear spatial distribution pattern. The mean bioaccumulation factor order was plankton (2.3 ± 1.8) > periphyton (1.3 ± 0.9) > macrophytes (0.7 ± 0.4) (KW = 55.09, p < 0.0001). Higher [THg] in water and bottom sediment were associated with high pH (R2adj = 0.118, p = 0.004) and organic matter (R2adj = 0.244, p < 0.0001). [THg] in macrophytes were positively influenced by [THg] in water (R2adj = 0.063, p = 0.024) and sediment (R2adj = 0.105, p = 0.007). [THg] in periphyton are positively related to forest fires (R2adj = 0.156, p = 0.009) and [THg] in macrophytes (R2adj = 0.061, p = 0.03) and negatively related to lake depth (R2adj = 0.045, p = 0.02). The transfer of Hg from water and sediment to the biota is limited. However, the progressive increase of the bioaccumulation factor between macrophyte, periphyton, and plankton may indicate Hg biomagnification along the food chain of the Araguaia River floodplain.