Long-term fixed passive acoustic monitoring of cetacean populations is a logistical and technological challenge, often limited by the battery capacity of the autonomous recorders. Depending on the research scope and target species, temporal subsampling of the data may become necessary to extend the deployment period. This study explores the effects of different duty cycles on metrics that describe patterns of seasonal presence, call type richness, and daily call rate of three blue whale acoustics populations in the Southern Indian Ocean. Detections of blue whale calls from continuous acoustic data were subsampled with three different duty cycles of 50%, 33%, and 25% within listening periods ranging from 1 min to 6 h. Results show that reducing the percentage of recording time reduces the accuracy of the observed seasonal patterns as well as the estimation of daily call rate and call type richness. For a specific duty cycle, short listening periods (5–30 min) are preferred to longer listening periods (1–6 h). The effects of subsampling are greater the lower the species' vocal activity or the shorter their periods of presence. These results emphasize the importance of selecting a subsampling scheme adapted to the target species.