Current estimates of sediment and nutrient loads from the Tully–Murray floodplain to the Great Barrier Reef lagoon are updated by taking explicit account of flood events. New estimates of flood discharge that include over-bank flows are combined with direct measurements of sediment and nutrient concentrations in flood waters to calculate the loads of sediment and nutrient delivered to the ocean during 13 floods that occurred between 2006 and 2008. Although absolute concentrations of sediment and nutrient were quite low, the large volume of water discharged during floods means that they make a large contribution (30–50%) to the marine load. By not accounting for flood flows correctly, previous estimates of the annual average discharge are 15% too low and annual loads of nitrogen and phosphorus are 47% and 32% too low respectively. However, because sediments may be source-limited, accounting for flood flows simply dilutes their concentration and the resulting annual average load is similar to that previously estimated. Flood waters also carry more dissolved organic nitrogen than dissolved inorganic nitrogen and this is the opposite of their concentrations in river water. Consequently, dissolved organic nitrogen loads to the ocean may be around twice those previously estimated from riverine data.