The self-fertilizing mangrove rivulus, Kryptolebias marmoratus, is an amphibious fish capable of reversible gill remodelling when moving between aquatic and terrestrial environments. In this thesis I determined how plastic morphological and physiological respiratory traits were integrated during transitions between environments. In two isogenic lineages, I found that behaviour (increased emersion) of individual fish caused gill morphological changes (enlargement of the interlamellar cell mass (ILCM)) that reduced gill surface area. I also found that large ILCMs that formed after 7 d of air exposure increased both gill ventilation and critical oxygen tension (Pcrit) when fish returned to water. These results indicate that large ILCMs reduce aquatic respiratory function, and increased gill ventilation was unable to maintain oxygen uptake at extreme levels of hypoxia. Ultimately, this study highlights the trade-offs in gill structure and function during the transition between air and water, and demonstrates that differences in behaviour can generate morphological variation.