Fatty acid (FA) composition and stable isotope (d13C, d15N) signatures of four aquatic plants, plankton, sediment, soil and suspended particulate organic matter (SPOM) collected from open floodplain lakes (Várzea) and rivers of the central Brazilian Amazon basin were gathered during high and low water stages in 2009. SPOM from Várzea had a major contribution of autochthonous material from phytoplankton and C3 aquatic plants. As shown from stable isotope composition of SPOM (d13C -31.3 ± 3.2‰; d15N 3.6 ± 1.5‰), the C4 aquatic phanerogam (d13C -13.1 ± 0.5‰; d15N 4.1 ± 1.7‰) contribution appeared to be weak, although these plants were the most abundant macrophyte in the Várzea. During low water season, increasing concentration of 18:3¿3 was recorded in the SPOM of lakes. This FA, abundant mainly in the Várzea plants (up to 49% of total FAs), was due to the accumulation of their detritus in the ecosystem. This dry season, when connectivity with the river mainstem was restricted, was also characterized by a high concentration in the SPOM of the cyanobacteria marker 16:1¿7 (up to 21% of total FAs). The FA compositions of SPOM from the Amazon River also exhibited significant seasonal differences, in particular a higher concentration of 16:1¿7 and 18:3¿3 during the dry season. This suggests a seasonal contribution of autochthonous material produced in Várzea to the Amazon River SPOM.