The mating system of self-compatible plants may fluctuate between years in response to ecological factors that cause variation in the deposition of self pollen vs. outcross pollen on stigmas. Such temporal variation may have significant ecological and evolutionary consequences, but it has rarely been studied, and the mechanisms that mediate temporal variation have almost never been investigated. We tested for variation in the proportion of seeds self-fertilized (s) between two years within 19 populations of the short-lived herb Aquilegia canadensis. Selfing varied widely among populations (range in s = 0.17-1.00, mean s = 0.82) but was inconsistent across years, indicating significant temporal variation. Three populations exhibited especially wide swings in the mating system between years. Mean s did not decrease with increasing population size (N), nor was the fluctuation in s associated with mean N or the change in N. As expected, s declined with increasing separation between anthers and stigmas within flowers (herkogamy), and s fluctuated to a greater extent in populations with more herkogamous flowers. Self-compatible plants can experience wide temporal variation in self-fertilization, and floral traits such as herkogamy may mediate temporal variation by forestalling self-pollination and thus allowing outcrossing during periods when pollinators are frequent.