Robust information on animal distributions and foraging behaviour is required to target management and conservation measures for protected species and populations. Visual survey data are commonly used to model these distributions. However, because visual data can only be collected in daylight, modelled distributions and consequent management actions may fail to identify or protect important nocturnal habitats. We explored this issue using data from the Moray Firth, Scotland, where visual survey data have previously been used to characterise habitat use and distribution patterns of harbour porpoises Phocoena phocoena. Marine predators such as harbour porpoises have a widespread distribution, are highly mobile and are known to exhibit behavioural variation in relation to diel cycles. Here, we used long-term passive acoustic data which revealed habitat-specific differences in diel patterns of detection. Harbour porpoises were detected consistently during night and day in sandy areas, with peaks in detection around sunrise and sunset, and at night in muddy areas. Detections also varied with depth, with the greatest proportion of daytime detections recorded in shallower sandy areas, and the most nighttime detections recorded in deeper muddy areas. The proportion of detections with foraging buzzes increased slightly during the night and in muddy habitats. These findings suggest that the importance of muddy habitats could be underestimated when using visual survey data alone. This highlights the value of using a combination of visual and acoustic methods both to characterise species distribution and to support efforts to develop appropriate spatio-temporal management of key habitats.