Winegrape growers in Napa Valley, California install nest boxes to encourage the presence of barn owls, natural enemies thought to provide vertebrate pest control services. Barn owls in this system select wooden nest boxes at least 3 meters high, with high proportions of grasslands surrounding the nest box. According to the adaptive breeding-habitat selection hypothesis, these habitat preferences should be adaptive, with increased fitness in preferred habitats. We found only modest association between reproductive success and nest box preferences, with substantial unaccounted variation in annual reproduction. Variation in the intrinsic quality of individual owls could also contribute to annual reproductive success, so we tested the hypothesis that habitat preferences and measures of intrinsic quality better predict reproductive success than either does alone. We measured annual reproductive success as the number of offspring that approached fledging age. Data on morphometrics, age, and breast plumage variation on adults served as measures of intrinsic quality of adults. Annual reproductive success served as the response variable in Generalized Additive Models, predicted by observed habitat preferences and measures of intrinsic quality. We found varying strength of association between the response variable and predictors, further emphasizing the complexity of annual reproductive success.