The analysis of physicochemical variables and selected dissolved elements was performed on the Apure River waters for 15 months. The variables pH, alkalinity, dissolved O2, conductivity and Na, Ca, Mg and Cd concentrations showed maximum values during low water, whereas K, Si, Fe, Al, Mn, Zn, Cu, Cr and dissolved organic carbon (DOC) showed maximum concentrations during rising and high water. Five important factors were found to control the amount and temporal variability of the dissolved elements: lithology, hydrology, vegetation–floodplain processes, redox conditions and organic complexation. Weathering of silicates, carbonates and evaporites in the Andes provides most of the proportion of Na, Ca, Mg and HCO3− to waters. The temporal variability of these ions is controlled by a dilution process. Although Si can be taken up by the biomass, Si and K can be leached from the floodplain by weathering of clays. Microbial decay of the submerged plants in the floodplain during the inundation periods provides DOC and K to river waters and changes the redox conditions in water. The changing redox conditions control the solubility of Mn, Zn and Fe. Dissolved Mn is a function of pH-dependent redox process, whereas Zn solubility is controlled by scavenging of Zn during the oxidation of Mn2+ to MnO2. Positive relationships between Al, Fe, Cu, Cr and DOC suggest that these elements are complexed by organic colloids generated in the floodplain. Moreover, the binding capacity of Fe with DOC increases under reducing conditions. Although Cd seems to be provided by weathering in the Andes, several processes can affect the mobility of Cd during transport. Copyright © 2010 John Wiley & Sons, Ltd.