Extreme or seasonal climatic events can lead to abrupt changes in environmental conditions. These events can produce a range of organismal responses that may help to protect local-scale populations against changes in climate. Empirical studies examining intraspecific variation in reproductive and physiological responses to varying durations of environmental stress are rare. We performed laboratory experiments under varying episodic and chronic salinities using the botryllid ascidians, Botrylloides nigrum and Botryllus planus. Our study illustrates intraspecific phenotypic variation to salinity stress. Respectively 40 and 20% of B. nigrum and B. planus colonies exhibited a distinct physical behavior when exposed to low salinity treatments. They distended their cloacal cavities, exposing their pharyngeal baskets and neural glands. Physiological signs of salinity stress included higher mortality, lower heart rates and limited asexual reproduction in both species. The physical and physiological differences among clones and colonies highlight phenotypic variation within and between genotypes to selective environmental pressures in real time. Our results underscore the need to examine physiological responses of species under
varying durations of environmental stress. Plastic responses of species to fine-scale environmental change may aid their persistence in a future where extreme climatic events are likely to be more common and acute.