The long-term sustainability of ex situ animal populations requires coordination across facilities through cooperative breeding programs. Here, we investigate the reasons for inconsistent reproductive success in the zoo-based North American Asian small-clawed otter (ASCO; Aonyx cinereus) population. Reproductive viability analysis (RVA) was used to identify which characteristics of ASCOs in breeding pairs were most predictive of reproductive success. The RVA identified pair type, contraception history, and age as the most significant predictors of offspring production. The use of deslorelin in males and long-term deslorelin use in females hinder future reproductive potential and should, therefore, be considered carefully in genetically valuable individuals and potential breeders. Moreover, genetically valuable animals should be paired with younger mates, as advancing male and female age decreases the likelihood of success. The lack of reproductive success observed after 1 year of attempted breeding among new pairs provides evidence of potential mate incompatibility, therefore, population managers should consider splitting up pairs that remain unsuccessful over time, because the likelihood of offspring production is low. Lastly, the inclusion of dens and/or caves and pools designed with ample shallow water areas in ASCO habitats may improve breeding success.