Resumo. AIM: Floodplains occupy a vast area of the Amazon basin but little is known of how their physical and limnological characteristics respond to local and regional ecological processes. In the Negro River basin and its main tributary, the Branco River, there are large areas that are seasonally flooded by water from local rainfall and that are not directly connected to major rivers. One such area is the floodplain of Viruá National Park, in Roraima state, northern Brazil. METHODS: The physical and chemical limnological characteristics of 19 plots in this area were monitored over three years (2008‑2010), with samples collected each year at the beginning and end of the rainy season (May to August). RESULTS: The water bodies studied had low mean values for electrical conductivity (22.0 ± 14.0 µS*cm-1) and pH (4.8 ± 0.7), relatively high temperatures (26.6 ± 2.7 °C), and moderate values for dissolved oxygen saturation (43.0 ± 21.5%) and water transparency (87.9 ± 38.7 cm). There was no significant difference in the limnological characteristics of the aquatic plots between the beginning and end of the rainy seasons in 2008 and 2010, but there were significant differences in 2009 due to an atypical rainfall pattern with two short dry spells during the rainy season. Multivariate analysis showed that the highest temporal variations in the limnological characteristics of the aquatic plots resulted from changes in water transparency, and these changes were related to soil type, elevation of the plot, and the particular micro-basins to which they were connected. CONCLUSIONS: This dynamic is different from that of most floodplains in the Amazon region, where the limnological pattern is well-defined seasonally and strongly dependent on the direct connectivity to large river systems. Floodplains not connected to large rivers should receive special attention in relation to the expected impacts of global climate change because of their high dependence on local rainfall.