Tristyly is a genetic polymorphism in which populations are comprised of three floral morphs (mating types) differing reciprocally in sex-organ height. Intermorph (disassortative) mating governed by a trimorphic incompatibility system should result in 1:1:1 morph ratio at equilibrium, but both deterministic and stochastic processes can cause skewed morph ratios in tristylous populations. Here, we investigate mechanisms causing morph-ratio bias in Pontederia parviflora, an emergent aquatic native to tropical America. We compared reproductive traits among morphs and surveyed 71 populations to determine patterns of morph-ratio bias. We then used simulation models of morph-frequency dynamics to test the hypothesis that morph-specific differences in pollen production and their influence on male fertility can explain patterns of morph-ratio bias. Ninety-seven percent of populations that we sampled were tristylous, but with a significant excess of the short-styled morph and a deficiency of the long-styled morph. Atypically for a tristylous species, mid-level anthers of the short-styled morph produced over twice as much pollen compared with the corresponding anthers of the long-styled morph. Our computer models incorporating this difference in male fertility resulted in morph ratios not significantly different from the average frequencies from our survey suggesting that the short-styled morph is more successful than the long-styled morphs in siring ovules of the mid-styled morph. We propose that the difference in male fertility between morphs may be a non-adaptive consequence of a developmental constraint caused by the architecture of tristyly in Pontederiaceae.