Intensity and types of land use have changed rapidly in the last century and in north-western Alberta this has coincided with the decline of Wapiti River watershed Arctic Grayling (<italic>Thymallus arcticus</italic>) populations. Data on diurnal dissolved oxygen (DO), chemical and physical stream habitat data were collected in nine sub-watersheds of the Wapiti River with historically abundant Arctic Grayling populations. Levels and fluctuations of DO and temperature were related to the status of populations; five of the nine streams had higher temperatures and lower DO during summer, anoxic conditions during winter and extirpated populations. Amount of disturbed land and road density within sub-watersheds were inversely related to DO levels and population status. Cumulative effects modelling suggests a possible mechanism for these relationships is increased phosphorous runoff, leading to impaired habitat. These relationships and thresholds may be used as a management tool to maintain or restore Arctic Grayling and other stream fishes.