Diel activity of two threatened freshwater fishes, a palaemonid prawn and an atyid shrimp, was established from remote underwater video in a pool of an upland stream (Australian Captial Territory). Both threatened fishes, Macquarie perch (Macquaria australasica) and two-spined blackfish (Gadopsis bispinosus), were diurnal while in the early-juvenile-phase (< 5 cm total length (TL)). In contrast, larger fishes (> 5 cm TL), shrimps and prawns were crepuscular and nocturnal. Additionally, subsampling of video was shown to be an efficient means of establishing the diel activity patterns of early-juvenile-phase fishes. The suitability of using underwater video to quantify short-term (seconds) behavioural interaction between individuals was also demonstrated, with early-juvenile-phase G. bispinosus exhibiting interference competition on 35% of occasions when two or more individuals were observed. An attempt to investigate trout predation on early-juvenile-phase M. australasica was unsuccessful, as these species were not recorded simultaneously. This study demonstrates that remote underwater video is a useful method for observing the in-stream behaviour of threatened freshwater fauna where other techniques are not viable.