In contrast to many small, mountainous watersheds in temperate coastal regions, where fluvial discharge and wave energy commonly coincide, deposition and reworking of tropical flood sediment can be seasonally decoupled, and this has important implications for coral-reef ecosystems. An understanding of the interaction between tropical flood sedimentation and wave climate is essential to identifying and mitigating effects of watershed changes on coral reefs as urbanization and climate change proceed. Sedimentary facies and isotopic properties of sediment in Hanalei Bay, on the island of Kaua'i, Hawai'i, USA, were used to assess deposition and reworking of flood deposits from the Hanalei River in a case study demonstrating the potential ecosystem effects of runoff from a steep, tropical watershed. In Hanalei Bay, the youngest and thickest terrigenous sediment was consistently present near the river mouth and in a bathymetric depression that acted as at least a temporary sediment sink. During this 2 yr study, the largest flood events occurred in late winter and spring 2006; substantial terrestrial sediment delivered by those floods still remained in the bay as of June 2006 because oceanic conditions were not sufficiently energetic to transport all of the sediment offshore. Additional sediment was deposited in the bay by a summer 2006 flood that coincided with seasonal low wave energy. In most years, flood sediment accumulating in the bay and on its fringing reefs would be remobilized and advected out of the bay during winter, when the wave climate is energetic. Turbidity and sedimentation on corals resulting from late spring and summer floods during low wave energy could have a greater impact on coral-reef ecosystems than floods in other seasons, an effect that could be exacerbated if the incidence and sediment load of tropical summer floods increase due to urbanization and climate change.