Resource competition among flowers is expected to influence variation in seed output within inflorescences, but the extent to which flower position affects competitive interactions is still incompletely understood. To investigate position effects on seed output in the perennial, monoecious macrophyte Sagittaria trifolia, we compared components of seed production (fruit set, seed number per fruit, and seed size) in control inflorescences to that in inflorescences from which half of the female flowers were experimentally removed, either from basal positions, from upper positions, or from across the inflorescence. Basal and upper flower removal reduced total seed output per inflorescence, while the throughout removal treatment maintained a seed yield comparable to the control. There was some increase in different reproductive components in each removal treatment and the magnitude of this increase depended on the positions of the flowers removed. Basal flower removal led to a higher number of seeds per fruit, whereas upper flower removal resulted in an increased fruit set, which successfully provided partial compensation for seed production. In the throughout removal treatment, both fruit set and seed set improved significantly, achieving full compensation compared to the control. The results indicate that resource competition is strongest among flowers belonging to the same whorl, and that the potential for reallocation of resources among whorls varies with flower position in S. trifolia. The results demonstrate the need to consider position effects for an understanding of factors driving variation in resource allocation and fruit production in plant populations.