Observation bias from methodological inconsistencies plague many long-term ecological monitoring studies, leaving land managers to question the validity of apparent population trends over time. Furthermore, some species are cryptic and have low detectability, so assessments are naturally imprecise. We assessed the utility of aerial surveys for woodland caribou from 1972 to 2009 at a Canadian national park in detecting a reliable population trend for this threatened species. The surveys varied in flight patterns, total distance flown, observer experience, speed, altitude, timing, temperature, and snow depth. Of these, distance and the speed/altitude index influenced the population estimates, whereas no variables influenced the calf:female ratio or winter range size. Year was included in all plausible models for population estimates, and the majority of plausible models for calf:female ratio and winter range size. Population size, recruitment and winter range size all declined over time in the respective models with the lowest AICc. Switching methodologies mid-way through a long-term aerial survey monitoring program creates greater complexity for trend analysis over time; however, this study suggests that reliable conclusions can still be drawn from long-term monitoring data if confounding factors are accounted for in the analysis. © 2014 The Wildlife Society.