Investigating the physiological state of wild salmonids is challenging on many levels.The sensitive nature of an integrated physiological stress response directs how biological data is collected in the field and, consequently, how the results are interpreted. This thesis is comprised of two main components. The first component encompasses laboratory-based studies addressing the potential confounding effects of: 1) anaesthesia with either tricaine methanesulphonate Electroshocking is an acute stressor from which juvenile chinook salmon can recover physiologically (usually within 12-24 h). Handling without shocking, however, significantly reduced serum lysozyme activity for up to 2 wks post-stress. Radiographs indicated that while 11 some degree of spinal abnormality exists naturally in domestic chinook juveniles, individuals exposed to a single brief shock incur significantly more spinal deformities.Some of the variation in the stress physiology and non-specific immune function of wild bull trout in the Torpy River system were explained by the combined effects of stream gradient, discharge rate, and riparian canopy-closure. The physiological measurements of wild bull trout generally did not differ from those reported in the literature for other salmonid species. The "background" effects of these habitat features on the physiology of wild salmonids must be considered when interpreting field-collected data.