Animals' selection of environments within a preferred range is key to understanding their habitat selection, tolerance to stressors and responses to environmental change. For aquatic animals, preferred environmental ranges can be studied in so-called shuttle-boxes, where an animal can choose its ambient environment by shuttling between separate choice chambers with differences in an environmental variable. Over time, researchers have refined the shuttle-box technology and applied them in many different research contexts, and we here review the use of shuttle-boxes as a research tool with aquatic animals over the past 50 years. Most studies on the methodology have been published in the latest decade, probably due to an increasing research interest in the effects of environmental change, which underlines the current popularity of the system. The shuttle-box has been applied to a wide range of research topics with regards to preferred ranges of temperature, CO 2, salinity and O 2 in a vast diversity of species, showing broad applicability for the system. We have synthesized the current state-of-the-art of the methodology and provided best practice guidelines with regards to setup, data analyses, experimental design and study reporting. We have also identified a series of knowledge gaps, which can and should be addressed in future studies. We conclude with suggesting some obvious directions for research using shuttle-boxes within evolutionary biology and behavioural and physiological ecology.