Landscape-driven processes impact the magnitude and direction of cross-ecosystem resource subsidies, but they may also control consumers' numerical and functional responses by altering habitat availability. We investigated effects of the interaction between habitat availability and subsidy level on populations of a riparian fishing spider, Dolomedes aquaticus, using a flood disturbance gradient in the Waimakariri River catchment, New Zealand. D. aquaticus predominantly eat aquatic prey as they hunt from the water surface. However, D. aquaticus biomass peaked at rivers with intermediate flood disturbance, rather than at less flood-prone rivers where the biomass of aquatic insect prey was markedly higher. Flooding positively influenced spider habitat quality, and an experimental manipulation at stable rivers indicated that unembedded cobbles, preferred D. aquaticus habitat, were a limiting factor, preventing response to the increased prey resource at stable sites. Potential terrestrial prey abundance was low, did not vary across the disturbance gradient, and is likely to have been a much smaller component of the fishing spiders' diet than aquatic insect prey. Thus landscape-driven factors not only controlled the magnitude of resource subsidies, but also influenced the ability of consumers to respond to them by altering the physical nature of the ecosystem boundary.