Long-term research provides a unique perspective on environmental processes, dynamics of populations and communities of organisms, and emergent properties of ecosystems. Many key ecological relationships can be obscured in short term studies by common features such as time lags, natural variability, nonlinear relationships, interactive drivers, or relatively slow processes. Aquatic ecosystems have yielded major scientific discoveries through long-term research, through both observational and experimental studies. These research results have ranged from the detection of multi-decadal climate oscillation effects on ecosystems to finer-scale understanding of the trophic and biogeochemical pathways through which nutrient pollution affects water quality. In this special issue of Limnology and Oceanography, the contributing authors demonstrate that—whether designed for the monitoring of managed natural resources, to answer fundamental scientific questions, or both—long-term research enables researchers to move far beyond their initial questions as unexpected dynamics are revealed over time. With the widespread maturation of long-term data sets and rapid emergence of new technologies that enhance research capabilities, opportunities for synthesizing knowledge are now creating unprecedented opportunity for scientific discovery that builds on this legacy of long-term aquatic research.