In Alberta, Canada, and throughout its North American range, Arctic Grayling (Thymallus arcticus) populations are rapidly declining. As part of monitoring and recovery planning, sampling protocols currently require direction for consistency and cost effectiveness. We assessed whether common sampling techniques, backpack electrofishing and angling, could reliably detect the presence and determine abundance estimates of the species in wadeable tributary streams of the Athabasca River. Additionally, we report on the use of a novel technique, egg-kick surveys, to detect spawning habitat and monitor abundance. Backpack electrofishing and angling with dry flies had the highest detection probabilities, although CPUEs were generally low. Egg-kick surveys rarely detected Arctic Grayling and generally failed as a monitoring tool in our study streams. We found that the size structure of catches were subject to temporal biases (early versus later summer) and dependent on gear type. As expected, angling detected more large fish (>110 mm) and included both juveniles and adults. We recorded about 3.1 times more large Arctic Grayling/km of angling versus backpack electrofishing. Young-of-the-year were more easily detected using backpack electrofishing in late summer (July–August). We were unable to calculate and compare abundance estimates derived from mark-recapture and three-pass removal methods because both techniques generally failed to meet literature-derived criteria and produced unreliable estimates. Our research emphasizes some of the challenges in formulating effective stream sampling protocols for monitoring a declining species characterized by low densities and patchy distributions.