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Dissolved organic carbon (DOC), lignin biomarkers, and the optical properties of dissolved organic matter (DOM) were measured in the Epulu River (northeast Democratic Republic of Congo) with the aim of investigating temporal controls on the quantity and chemical composition of DOM in a tropical rainforest river. Three different periods defined by stages of the hydrologic regime of the region, (1) post dry flushing period, (2) intermediary period, and (3) start of the dry period/post flush, were sampled. Temporal variability in DOM quantity and quality was observed with highest DOC, lignin concentration (Σ8) and carbon‐normalized (Λ8) values during the flushing period attributed to greater surface runoff and leaching of organic‐rich horizons, with lowest values in the dry period/post flush once source materials were well leached. Chromophoric DOM (CDOM) was strongly correlated to DOC and Σ8 (r2 = 0.85 and 0.83, respectively; p < 0.001), and CDOM quality measurements (SUVA254, spectral slope ratio and fluorescence index) were strongly correlated to Λ8 values (r2 = 0.77, 0.69, and 0.75, respectively; p < 0.001), demonstrating the ability to derive DOC and lignin export and to track DOM quality in tropical riverine systems from simple optical measurements. This study demonstrates similar effects in the variability of DOM quantity and quality due to changing hydrologic inputs for a tropical river as has been previously reported for temperate and northern high‐latitude rivers. Therefore, flushing periods in tropical rivers warrant further study, as they are critical toward understanding ecosystem biogeochemistry as maximal export of freshly leached plant material occurs during this time period.