Nursery habitat requirements for age-0 Esox spp. in the upper St. Lawrence River are well understood; however, little is known about the influence of physical habitat on their spatiotemporal ecology during fall and winter periods. A hatchery study evaluated biologically relevant endpoints post-implantation of a mini-acoustic transmitter in age-0 Muskellunge. Neither tag expulsion nor mortality were observed, nor influence of tag presence on short-term growth rates. Applying this tool to evaluate their ecology, I captured and tagged age-0 Muskellunge (Esox masquinogy) and Northern Pike (Esox lucius) from August to October in natal bays. Detection data, modeled against environmental covariates, found deeper littoral regions were used by both species, and complex interactions between covariates influenced spatial trends during this critical period. With similar overwintering spatial ecology between these congeneric competitors, overwintering microhabitat use studies in association with water level management may confirm habitat overlap and inform wetland restoration efforts.