Studies of fine scale habitat characteristics associated with age-0 muskellunge (Esox masquinongy) are uncommon and those that have been conducted have relied on targeted, nonrandom sampling designs which may bias study results. We used a random design to sample age-0 muskellunge and shallow water (< 13. m) habitat features found in the upper Niagara River, New York, during late July through early September 2013-2105. Comparisons of habitat features between sites where muskellunge were present and absent and Firth logistic regression were used to identify important characteristics of muskellunge nursery locations. A total of 15 age-0 muskellunge were collected at 11 of 295 sites sampled. Vallisneria americana was the dominant aquatic vegetation at 10 of 11 sites where muskellunge were collected and sand and mud were the dominant substrate sizes at all locations where age-0 muskellunge were collected. The probability of age-0 muskellunge presence was positively related to the proportion of the water column occupied by aquatic vegetation. Despite sampling nearly 300 sites, the small number of age-0 muskellunge collected limited the types of analyses that could be performed. However, our results provide evidence that shallow water areas with abundant V. Americana should be conserved or resortred to provide reaering habitat for muskellunge in the upper Niagara River. IN future studies, samples sizes of age-0 muskellunge in the upper Niagara River. In future studies, sample sizes of age-0 muskellunge may be increased while maintaining a probability sampling design, by randomly sampling within pre-defined areas that contain habitat features identified at sites where muskellunge were present in our study.