Large rivers have a strong influence on the Arctic Ocean, but little attention has been given to the biogeochemical effect that lake-rich delta floodplains may have on river waters prior to marine discharge. We assessed the effect of the Mackenzie Delta on riverine fluxes of nutrients and organic matter to the Arctic Ocean during the open water period of 2004. Using a new estimate of peak off-channel water storage in the delta floodplain, a two-source mixing model was developed (channel water plus recovery of off-channel water) to estimate the volume-weighted nutrient composition of river water after the off-channel water was recovered from the delta during the hydrograph recession period. Results with the delta effect included (i.e., with recovery of off-channel water) relative to results with the effect omitted (i.e., analogous to historical monitoring upstream of the delta) show particulate levels were 10–18% lower, but enriched in organic content (POC:TSS, PN:TSS, PP:TSS) by 75–280%; dissolved inorganic nutrients were lower (NO3– 14%; SRP 14%; SRSi 5%) except for ammonium (10%); and dissolved organic matter was higher (DOC 15%; DON 62%; DOP 239%). The resulting nutrient quality (C:N:P stoichiometry) was more enriched in carbon (TOC:TP) by 79% and in nitrogen (TN:TP) by 77% relative to phosphorus. Model results were compared against nutrient measurements throughout the delta channel network taken three times over this same period, and differences from upstream to downstream matched reasonably well to the model, though they also suggested the delta effect may be more complex than represented by the model. Our results generally indicate the Mackenzie Delta has an important effect on the magnitude and quality of riverine particulates and nutrients prior to entering the sea. Such an effect has not been quantified in prior work and is likely to be important in other arctic rivers with lake-rich deltas. Our enhanced sampling of the high-discharge period during early hydrograph recession has also better captured the detailed composition of C, N, and P constituents in the river water, ultimately leading to improved estimates of nutrient levels and overall nutrient quality for the open water period that differ appreciably from prior observations on the Mackenzie River.