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Context: Oysters provide structured habitat along coastal margins, but owing to the high turbidity of many estuaries, characterising the faunal communities that utilise oyster reefs typically requires direct capture, which is potentially lethal or destructive. Acoustic imaging sonar can non-destructively sample the abundance and size of swimming organisms (nekton), but collection of data from acoustic imaging files requires substantial processing time following field sampling. Aims: We compared five alternate data examination protocols that could be applied to acoustic imaging files from intertidal oyster reefs and identified a protocol (analysing randomly chosen 3 of 5 min of imagery recordings) that reduces parameter estimation bias and processing time. Methods: To demonstrate the utility of this protocol, we investigated diel differences in fish use of fringing oyster reefs. Key results: During day-time and night-time sampling, we respectively recorded 4535 and 1924 fish across a size range of 1–52 cm. We found no difference between day and night in relative abundance, mean size, or size-spectra of the fish community inhabiting reefs. Conclusions and implications: Active acoustic imaging can be an effective, non-destructive method to characterise faunal communities in shallow, turbid habitats and can be used to test hypotheses regarding the ecology of these ecosystems. Sampling the mobile fauna that use oyster reefs as habitat is difficult because of the complex nature of the reef and the often turbid conditions found within estuaries. We used acoustic imaging sonar to estimate abundance and size of fishes on fringing, intertidal oyster reefs in South Carolina, USA, and recommend a data processing protocol to standardise future studies utilising this promising, non-lethal sampling methodology. [ABSTRACT FROM AUTHOR]