Invasive species present a global threat to the conservation of biodiversity. When invasive and endangered native taxa hybridize, the resulting admixture introduces novel conservation challenges. Across a large region of central California, a hybrid swarm consisting of admixed endangered California tiger salamanders (CTS) and introduced barred tiger salamanders (BTS) has replaced native populations, threatening the genetic integrity of CTS and the vernal pool systems they inhabit. We employed a large‐scale, genomically‐informed field experiment to test whether shortening breeding pond hydroperiod would favor native CTS genotypes. We constructed 14 large, semi‐natural ponds to evaluate the effect of hydroperiod duration on larval survival and mass at metamorphosis. Earlier work on this system has demonstrated hybrid superiority under many conditions, and suggested that hybrids are favored in human‐modified ponds with artificially‐long hydroperiods. Consistent with these earlier studies, we found overwhelming evidence for hybrid superiority. Very short hydroperiods substantially reduced the mass (1.1‐1.5x) and survival probability (10‐13x) of both native and hybrid larvae, confirming that hydroperiod likely exerts a strong selective pressure in the wild. We identified 86 candidate genes, representing 1.8% of 4,723 screened loci, that significantly responded to this hydroperiod‐driven selection. In contrast to earlier work, under our more natural experimental conditions, native CTS survival and size at metamorphosis were always less than hybrids, suggesting that hydroperiod management alone will not shift selection to favor native larval genotypes. However, shortening pond hydroperiod may limit productivity of hybrid ponds, complementing other strategies to remove hybrids while maintaining vernal pool ecosystems. This study confirms and expands upon previous work which highlight the importance of hydroperiod management to control invasive aquatic species. We hope that the combination of extensive ecological knowledge, modern genomic approaches, and naturalistic experiments employed here can serve as a model for some of the complex invasion scenarios threatening global biodiversity.This article is protected by copyright. All rights reserved