Adaptational physiology studies how animals cope with their environment, even if this environment is subject to permanent fluctuations such as tidal or seasonal variations. Aquatic organisms are generally more prone to be exposed to osmotic, hypoxic and temperature challenges than terrestrial animals. Some of these challenges are more restraining in an aquatic environment. To date, very few studies have used in vivo magnetic resonance imaging (MRI) to uncover the physiological mechanisms that respond to or compensate for these challenges. This paper provides an overview of what has been accomplished thus far by using MRI to study the environmental physiology of fish. It introduces the reader to the use of small teleost fish such as carp (12 cm, 60 g) and eelpout (25 cm, 50 g) as models for such research and to provide new perceptions into the applicability of MRI tools based on new insights into the nature of MRI contrast. Representative MRI studies have made contributions to the identification of the lack of cell volume repair in stenohaline fish during osmotic stress. They have studied the underlying physiological mechanisms of brain anoxia tolerance in fish and have qualified the role of the cardio-circulatory system in setting thermal tolerance windows of fish.