Tracking and understanding variation in pathogens such as Batrachochytrium dendrobatidis ([Bd]), which causes amphibian chytridiomycosis and has caused population declines globally, is a priority for many land managers. However, there has been relatively little sampling of amphibian communities at high latitudes. We used skin swabs collected during 2005–2017 from boreal toads (Anaxyrus boreas; N = 248), in southeast Alaska (USA; primarily in Klondike Gold Rush National Historical Park [KLGO]) and northwest British Columbia (Canada) to determine how Bd prevalence varied across life stages, habitat characteristics, local species richness, and time. Across all years, Bd prevalence peaked in June and was >3 times greater for adult toads (37.5%) vs. juveniles and metamorphs (11.2%). Bd prevalence for toads in the KLGO area, where other amphibian species are rare or absent, was highest from river habitats (55.0%), followed by human-modified upland wetlands (32.3%) and natural upland wetlands (12.7%) — the same rank-order these habitats are used for toad breeding. No Columbia spotted frogs (N = 12) or wood frogs (N = 2) from the study area tested Bd-positive, although all were from an area of low host density where Bd has not been detected. Prevalence of Bd on toads in the KLGO area decreased during 2005–2015. This trend from a largely single-species system may be encouraging or concerning, depending on how Bd is affecting vital rates, and emphasizes the need to understand effects of pathogens before translating disease prevalence into management actions.