ii DedicationTo my parents for their patience and understanding while raising a child obsessed with the natural world. You never knew what creature you would find hidden somewhere in your house next, yet you never discouraged my curiosity. For that I am forever grateful. To the Wards and their ongoing support and encouragement. I am so fortunate to have joined such an amazing family. And finally, to my partner Taylor, to whom I simply say, thank you, thank you, thank you.iii Abstract While it is generally considered that habitat degradation negatively impacts resident fish, the physiological mechanisms behind this trend are not well understood.Applying scientific techniques to increase our understanding of how habitat influences individual physiology and how that, in turn, influences fish population dynamics is becoming an important approach to environmental monitoring. In Chapter 2, I quantify how watershed land use influences the over winter energy reserves and health of a small stream fish and demonstrate that land use influences these metrics differently for females and males of the model species. In Chapter 3, I investigate the parasite communities of juvenile fish residing in a range of impacted streams to identify potential bioindicators of habitatand consequently fishhealth. These data are the first of their kind for both species examined, and are also the first time these techniques have been used to address these unique research questions.iv