Spatial and temporal variation in relative density of 0+ and 1+ brown trout was examined over three summers in the Kakanui River, North Otago, New Zealand. Both 0+ and 1+ trout were distributed throughout the river. Spatial variation in relative density was much higher than annual variation. Within years, relative density of 0+ brown trout varied by 5 to 92 times between sites (mean coefficient of variation, CV = 1.08) and of 1+ trout by 18 to 84 times between sites (CV = 1.13). Mean relative density of 0+ brown trout varied by 1.5 to 2.0 times between years (CV = 0.35) and of 1+ trout by 3.6 to 23.2 times between years (CV = 0.96). The pattern of 0+ trout spatial distribution was not closely related to the distribution of redds (which also were distributed throughout the river) and not related to the distribution of benthic invertebrate food. By their second summer, most trout occupied the middle and lower reaches of the river. Mean length of both 0+ and 1+ trout increased with distance downstream. Floods greater than 290 m3s−1, and with a return period of 4 years, during the late incubation and early fry stages (August‐November) were associated with impaired recruitment, yet a large flood (816 m3s−1) in March 1994 had no apparent effect on the survival of 0+ trout 80–100 mm in length.