Biodiversity collections are experiencing a renaissance fueled by the intersection of informatics, emerging technologies, and the extended specimen. In this talk, we explore the enormous potential for transformative research in ecology using biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Like DNA, SIA provides a fundamental ‘currency’ interpreted in the context of biogeochemical and ecological principles. Integration and extension of specimens across regional biodiversity collections allows for evaluation of ecological change at decadal and continent-wide scales. We also discuss important challenges to SIA research in this context, including analysis of sparse samples, lack of isotopic baselines, and preservative effects. Key to harnessing the power of SIA is a centralized, searchable repository for isotopic data that links to digitized biodiversity data. The IsoBank Database Project is developing this resource to capitalize on big data analytics that interfaces with long-term environmental databases. The general framework could be further developed and explored in a research program that interfaces ecological observatory networks like NEON. We propose that the time is right to marshal biodiversity collections to provide important historical context to fundamental questions in freshwater ecological research, baselines for ecosystem monitoring following disturbance, and a quantitative means for assessing effects of ecosystem restoration.