Total (HgT), reactive (HgR) and organic (Hg ORG) mercury species have been quantified in non-filtered waters collected from the Negro River Basin, Amazon (from January/2002 through January/2004), in both black and white water bodies. Black waters presented the highest HgT, HgORG and HgR concentration (29.1 ng L-1, 1.63 ng L-1 and 3.9 ng L-1, respectively), while, white waters presented the lowest HgT, Hg ORG and HgR concentration (8.8 ng L-1, 0.49 ng L-1 and 1.2 ng L-1, respectively). An inverse correlation between HgT and the water level over the basin was obtained, although the HgORG concentration has increased in the first rainy months and then decreased as the water level rose. Total mercury in surface sediments (0-10 cm) ranged from 70 to 271 mg kg-1 being the methylmercury 0.47-1.79 % of this stock. The results indicate that HgR and the labile dissolved organic matter were introduced into the aquatic environment during the flooding season, especially in the earlier stages, thus contributing to mercury methylation. ©2007 Sociedade Brasileira de Química.