Understanding the flux and fate of nutrients and sediments from rivers is of global importance because of the effects of these materials on coastal ecosystems. The present study followed three flood events from upper tributaries of the Normanby River to Princess Charlotte Bay in the northern Great Barrier Reef (GBR) lagoon, Australia. During each event, nutrients and suspended sediment concentrations were measured along a freshwater to marine transect. The upper catchment provided the majority of suspended sediments and nutrients supplied to the river system, although concentrations of most materials decreased by 52–85% between the upper catchment and estuary. As an exception, ammonium concentrations doubled within the estuary, indicating that undisturbed coastal ecosystems can provide a significant source of dissolved inorganic nitrogen to tropical river flood plumes. The dissolved nutrients in floodwaters stimulated phytoplankton blooms that inundated seagrass meadows and coral reefs. Northern GBR marine ecosystems are increasingly threatened by climate change and catchment development. The results of this study show that increased anthropogenic loads of nutrients and sediments from the upper Normanby catchment have the potential to affect the condition of marine ecosystems at Princess Charlotte Bay.