Mercury (Hg) biomagnification in fish food chains is a relevant subject due to the high fish consumption of the Amazonian population and the high toxicity of this metal. In the Amazon, floodplain lake hydrodynamics change considerably along the four seasons of the hydrological cycle (rising water, high water, falling water and low water), which can influence Hg bioaccumulation in fish. The main aim of this study was to evaluate if Hg biomagnification is influenced by seasonality in a floodplain lake (Puruzinho Lake) in the Brazilian Amazon. Additionally, the influence of food chain modeling on measurement of Hg biomagnification was tested. Hg concentrations and stable isotope signatures (carbon and nitrogen) were estimated in four species, Mylossoma duriventre (herbivorous), Prochilodus nigricans (detritivorous), Cichla pleiozona (piscivorous) and Serrasalmus rhombeus (piscivorous). The “trophic magnification slope” (TMS) of the food chain composed by the four species was calculated and compared among the four seasons. There was no significant seasonal variation in TMS among rising water, high water, falling water and low water seasons (p = 0.08), suggesting that Hg biomagnification does not change seasonally. However, there was significant variation in TMS among different food chain models. Lower TMS was observed in a food chain composed of detritivorous and piscivorous fish (0.20) in comparison with a food chain composed of the four species (0.26). The results indicate food chain modeling influences TMS results.