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Increases in east Australian humpback whale populations, specifically in areas where sightings were previously infrequent, highlight the importance of understanding the usage patterns and habitat preferences for resting grounds along migration pathways. This study investigates the spatio-temporal distribution of humpback whales in Jervis Bay, Australia, based on pod composition, providing insight on the role of this shallow coastal embayment for mother-calf pods during the southern migration to polar feeding grounds. Geographical citizen science-based sighting data, collected from a commercial whale-watch platform during the 2007–2010 migration seasons, were used to examine variations in bay usage and pod composition. Differences in the distribution patterns of mother-calf and non-calf pod sightings were examined using spatial cluster analysis. The impact of sampling bias, introduced through non-specialist volunteer collected data, on spatial cluster detection was simulated. Observation error and spatial sampling bias may affect local spatial cluster detection. Sampling processes with potential to contribute to this bias should be recorded in the survey design of geographical citizen science based data collection programmes. Mother-calf pods showed a significant preference for the shallow waters of Jervis Bay during October and November, indicating the bay may function as a preferred resting location during their southern migration with important marine management implications.