Field measures were combined with synthetic aperture radar (SAR) images to evaluate the use of radar for estimating temporal biomass and mapping of aquatic vegetation in the lower Amazon. A SAR-based methodology was developed for quantification of the annual net primary productivity (NPP) of aquatic vegetation. The spatial variability of the canopy biophysical properties was detectable with radar data. The logarithmic relationship between backscattering coefficients and biomass suggested that (1) at low biomass, high transmissivity of the microwave radiation through the vegetation canopy occurred and the backscattering was a result of quasi-specular reflection of both C and L bands and a minor contribution of canopy volume scattering from C band; (2) at intermediate levels of biomass, moderate changes in backscattering values occurred and the backscattering saturation point was reached at 470, 660, and 620 gm^-2, for C band, L band, and the index, respectively; and (3) at high biomass, the transmissivity of C and L band radiation was equally attenuated and backscattering approached similar values for both. Complementary information of the satellites yielded classification accuracy higher than 95% for vegetated areas of the floodplain. After correction for seasonal biomass loss, the estimated annual NPP was 6350gm^-2 or 4.1x10^12g for the entire area. The estimated NPP of the aquatic vegetation yielded a total carbon uptake of 1.9x10^12 g C yr^-1. Calculations based on the estimated area of each habitat of the floodplain, and the productivity data suggested in the literature, resulted in a net carbon productivity from flooded forest, phytoplankton, and periphyton of 0.35x10^12gCyr^-1, 0.22x10^12 g C yr^-1, 0.07x10^12gCyr^-1, respectively. The total combined autochthonous annual net productivity of the study area was 2.5x10^12 g C, of which 75% was from C3 aquatic plants. This study represents the first attempt to develop a method to use SAR and field data for estimating spatial and temporal variations in biomass of aquatic vegetation from a natural floodplain.