Two ecological acoustic recorders were deployed in Southern Sri Lanka to study the presence of the assumed resident population of pygmy blue whales. A major shipping lane runs through this feeding area of the whales and it has been recognized by the International Whaling Commission as well as International Maritime Organization as a risk area for ship strikes. To implement any management practices to mitigate ship strikes, a solid scientific basis is needed. Such data must include information on migration and movement patterns of the whale population. Therefore, combining the passive acoustic monitoring data with existing visual transect survey results gives further insight to choosing suitable management practices to address the issue. Passive acoustic monitoring data indicate that at least part of the population is indeed resident in the area throughout the year but there is both seasonal and inter-annual variation in the acoustic activity of the whales. The acoustic data were further combined with data from oceanographic models and the results indicate there is no single parameter explaining the variation, although the acoustic activity has weak correlation with rainfall patterns. The pygmy blue whale call detections also appear to increase during periods of stronger upwelling in Southern Sri Lanka.