1. In the mid-1970s, Hynes (1975) wrote eloquently about the complex interactions between aquatic and terrestrial systems. Central theories in stream ecology developed thereafter have dealt with the longitudinal flow of energy, materials and organisms in streams, and, with the exception of the flood pulse concept (Junk, Bayley and Sparks, 1989), have largely ignored areas outside the riparian zone. The structure of the upland and activities occurring there play a more important part than previously recognized in regulating community structure and ecosystem processes in streams. 2. These new perspectives are made possible by developments in hierarchy theory, patch dynamics, and the refinement of tools used to quantify spatial and temporal heterogeneity. 3. Geographical information systems (GIS), image processing technology and spatial statistical techniques allow quantitative assessment of lateral, longitudinal and vertical components of the landscape that interact at several spatial and temporal scales to influence streams. When GIS is used in concert with geostatistics, multivariate statistics, or landscape models, complex relationships can be elucidated and predicted. 4. To a certain extent, the tools discussed above have only automated functions that were previously performed manually. This suite of tools has improved the ability of aquatic ecologists to examine relationships and test theories over larger, more heterogeneous regions than were previously possible. 5. At the local, state and federal level, management and regulatory frameworks are currently being re-evaluated to incorporate this new perspective in resource management and policy decision making. 6. We will discuss current and future trends in technologies and tools used for aquatic ecosystem research, and the use of techniques as they are applied in these regional assessments are also discussed.