We present a comprehensive dissolved rare earth element (REE) data set for the Amazon River and its main tributaries, Rio Negro, Solimões, and Madeira, as well as the Curuaí floodplain. The two‐year time series show that REE vary seasonally with discharge in each of the tributaries, and indicate a hydrologically dominated control. Upper crust normalized REE patterns are relatively constant throughout the year, with Ce/Ce* anomalies being positively related to discharge. We propose revised annual dissolved REE fluxes to the surface Atlantic Ocean based on an integration of the seasonal data. For Nd (<0.22 μm) this results in an average flux of 607 ± 43 T/yr, which is at least 1.6 times larger than the previous estimate of 374 T/yr (<0.45 μm) based on low water stage data. Moreover, during the high water season the maximum Nd flux measures 1277 t.yr⁻¹, constituting 30% of the required flux to the Atlantic Ocean (Tachikawa et al., 2003). Consequently, a smaller contribution of Nd from atmospheric and river particle desorption is required than was previously suggested. A mass balance of Amazon tributaries and observed fluxes at Óbidos indicates that dissolved LREE behave quasi‐conservatively. Conversely, the HREE mass balance presents a deficit during the high water stages, which could be related to the passage of water through the floodplain system accompanied by solid/dissolved phase transfer.