A major challenge for ecologists is understanding ecosystem dynamics and function under environmental and anthropogenic stresses. An approach for addressing this challenge is the analysis of the different components contributing to secondary production (i.e., consumer incorporation of organic matter or energy per time unit) and how this production is influenced by external factors. Production studies have been recognized as a powerful tool in aquatic ecology, with applications in energy–biomass flow studies, trophic ecology, management of biological resources, as well as assessment of environmental stress. In this paper, we summarize ideas and techniques related to the estimation of secondary production and discuss how this approach may be used to evaluate ecological change in aquatic ecosystems. We include a critical review of classical methods and empirical models to estimate secondary production and provide several applications of production studies to current stresses affecting aquatic ecosystems, such as climate change, pollution, and the introduction of non-indigenous invasive species. Our goal is to illustrate the advantages of using secondary production as a more integrative tool for the assessment of the ecosystem function, in particular when subjected to strong anthropogenic and climatic stress.