Recent declines of many seabird populations have placed increased emphasis on determining the status of potentially threatened species. However, the burrow-nesting habits and inter-annual fluctuation in breeding numbers of some species make trend detection difficult, and so knowledge of their population dynamics often remains coarse. Here we report observed fluctuations, and assess the efficacy of monitoring of sooty shearwaters (Puffinus griseus), on three islands in southern New Zealand between the breeding seasons of 1996–97 and 2004–05. Apart from a steady increase in burrow-occupant density at one island, few significant trends in abundance measures were detected. Considerable variation among individual sites within islands led to high uncertainty in island-wide trend estimates. Simulations showed that the measurements of occupant density have a limited ability of detecting all but very pronounced trends, whereas changes in burrow-entrance density are more likely to be detected. Annual fluctuations in the proportion of occupied burrows at individual sampling sites were highly synchronous within islands and reasonably synchronous between two of the islands, suggesting that breeding numbers are at least partly determined by broad-scale factors. The large declines in the abundance of sooty shearwaters reported from the late 1980s to mid-1990s appear not to have continued through our monitoring period. Lack of adequate within- and among-island replication, and short time series of data may severely reduce our ability reliably to detect population trends in many studies of burrowing Procellariiformes.