In many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities’ dynamics can be indirectly coupled by reciprocal among ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal of organisms. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.