Migratory species may be especially sensitive to climate change because their lifecycles are affected by dynamic ecological processes operating at global spatial scales. Insight into environmental effects upon en route decisions by migrants can therefore be a critical first step toward assessing their vulnerability to future climatic shifts. We extracted behaviour-related parameters from a recent formulation of multistate mark–recapture models, and used them to evaluate the importance of variation in local weather and broad-scale climate to decisions made by autumn passerine migrants at a coastal stopover site in Atlantic Canada. We found dramatic interannual fluctuations in the proportion of migrants that were transient (departing within a day of arrival), with annual average values ranging from 24% to 96% over the years 1996–2007. However, the relationships of stopover behaviour (transience and departure probability) to local weather (wind and precipitation) and to regional climatic fluctuations were similar across three distinct species groups and for birds of different fuel-loads, indicating the potential for both immediate (day-to-day) and long-term environmental influences (spanning several seasons). This cross-scale approach contributes valuable information toward the conservation of migrants in the face of a changing climate by (i) quantifying environmental influences on stopover behaviour in broad temporal and geographic contexts, and (ii) demonstrating largely parallel interannual variation in stopover site-use among birds with contrasting migratory timing and strategies.