This paper considers examples of how alterations to streams and rivers in their lower reaches can produce biophysical legacies in upstream reaches on levels from genes to ecosystems. Examples include: 1) genetic- and species-level changes, such as reduced genetic flow and variation in isolated upstream populations; 2) population- and community-level changes that occur when degraded downstream areas act as population ''sinks'' for ''source'' populations of native species upstream or, conversely, as ''source'' populations of exotic species that migrate upstream; and 3) ecosystem- and landscape-level changes (e.g., nutrient cycling, primary productivity, regional patterns of biodiversity) that can occur in headwater systems as a result of downstream habitat deterioration and hydrologic modifications.

Finally, a case study from my own research illustrates the importance of careful consideration of downstream-upstream linkages in formulating research questions, designing experiments, making predictions, and interpreting results. The effects of dams and associated water abstraction in lowland streams of Puerto Rico has forced my colleagues and me to re-evaluate the results of ecological research that we have conducted in highland streams over the past decade and to redirect our research to consider downstream-upstream linkages.