Genomic introgression among divergent taxa following human-mediated secondary contact is a growing concern for the management and conservation of aquatic biodiversity. We simulated the composition of taxa following admixture and hybridization by independently altering three variables: (1) initial proportion of parental taxa following secondary contact; (2) fitness gradients among parental and introgressant taxa; and, (3) strength of assortative mating among these taxa. Ultimately, we established that parental taxa will trend toward extinction as introgression proceeds in spite of even a heavy fitness penalty for the hybrids. Also, the number of generations required (rate) to reach an arbitrarily determined threshold of extinction (< 5.0%) was inversely related to the strength of the relative fitness gradients among parental and derivative hybridized lineages. Moreover, the rates of extinction for parental taxa depended on the initial relative proportions in the admixture with rare taxa going extinct more rapidly than abundant taxa. Finally, the strength of assortative mating (as an evolved or reinforced mechanism of pre-mating isolation) will affect the rate of extinction. Introgressive hybridization, therefore, emerges as an important risk to structural biodiversity wherever divergent, yet reproductively compatible, taxa come together naturally or are brought together through human activities.