The sources of spatial and temporal variation and rates of nutrient deposition via throughfall were studied for 9 months in the Anavilhanas archipelago of the Negro River, Brazil. A total of 30 events was sampled individually for rain and throughfall chemistry in a 1-ha plot of flooded forest. Throughfall samples were collected in 40 collectors distributed in five parallel transects in the study plot, while rain was collected in 4 collectors in an adjacent channel. Volume-weighted mean (VWM) concentrations of solutes in rain were consistently lower than in throughfall, except for H+, NO−3 and NH+4. Ratios of VWM concentrations of rain to throughfall indicated that K+, followed by Mg2+ and PO3−4, were the most enhanced solutes as rain passed through the forest canopy. The deposition of solutes varied significantly among transects, except for Na+ and Ca2+, and was significantly correlated with maximum flooding depth, foliar nutrient content soil fertility and canopy closure for most solutes. The concentrations of PO3−4 and most major ions were higher in throughfall compared to those in rain due to canopy exchange and dry deposition. In contrast, NO−3, NH+4 and H+ were retained due to immobilization by leafy canopy and ion exchange processes. Solute inputs via throughfall (not including stemflow) to a floodplain lake (Lake Prato) of the archipelago accounted for 30 to 64% of the total for most solutes in the lake at high water, which indicates that throughfall is an important source of nutrients to the aquatic ecosystem of the Anavilhanas archipelago.