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A passive-acoustic telemetry system was used for the first time for the fine-scale, three-dimensional tracking of individual cleaner fish in commercial Scottish salmon sea-pens in full commercial operation. The aim was to test the system performance and provide baseline data on the comparative distribution and swimming activity of individual ballan wrasse and lumpfish under standard farm practices with the long-term aim of informing stocking and husbandry strategies. In March 2015, wild ballan wrasse (Labrus bergylta) (115 ± 20 g; n = 13) and farmed lumpfish (Cyclopterus lumpus) (281 ± 42 g; n = 13) previously deployed in June–October 2014 were recaptured, implanted with acoustic tags pinging every 6–12 s and released into their original sea cage holding Atlantic salmon (Q2 2014; 2059 ± 35 g mean-weight). Control tags were deployed in cleaner fish hides to validate the system performance …