Remote, non-intrusive monitoring of elusive mammals remains problematic, particularly in running waters. The utility of using submerged infrared counters for monitoring non-intrusively the activity of Eurasian otters Lutra lutra was assessed in three tributaries of the River Dee (Beltie, Cattie, Feardar; Scotland) during 2003–2004. Otters passing through the infrared counters were strongly nocturnal and displayed a bimodal diel activity pattern. Seasonal activity indices varied fourfold between tributaries and peaked during the salmonid breeding season. The median time elapsing between consecutive night visits was 2.02±0.79 days and did not differ between tributaries. The median head–body length of adult otters was estimated at 75.0±1.1 cm, whereas median upstream swimming speed was calculated at 0.97±0.01 m s−1. Minimum census estimates revealed the activity of at least two adults in the Beltie, two adults and three juveniles in the Cattie, and two adults with one juvenile in the Feardar. Our study indicates that, under suitable conditions, infrared technology can be used effectively to examine non-intrusively the activity of free-ranging otters in running waters, offering some advantages over previous, more intrusive techniques that relied on the collection of spraints, the use of radioisotopes or the tracking of marked individuals.