The planktonic species Eurytemora affinis and the benthic species Tigriopus japonicus are two copepods that are extensively employed in aquaculture operations, especially as a source of live feed during larval rearing. Compared to T. japonicus, E. affinis is difficult to keep in stable cultures and to mass produce, which largely limits its usage. Furthermore, high levels of un-ionized ammonia (NH3−N) can limit the productivity of aquatic organisms. However, the toxicity of NH3-N can be easily affected by environmental conditions. The planktonic and benthic growth features of E. affinis and T. japonicus may reflect different adaptations to NH3−N stress that could affect their reproductive performances. Hence, we investigated the effect of NH3−N on the survival and reproductive patterns of E. affinis and T. japonicus at both the individual and population levels. The median lethal concentrations for both the nauplius and copepodite stages, life history parameters, and population growths of each species were evaluated after acute (24-h) and chronic (21–28 days) NH3−N exposure. The results showed that E. affinis was more vulnerable to NH3−N stress than T. japonicus at all developmental stages. The nauplius and copepodite stages of E. affinis exhibited 14.7- and 33.7-fold lower 24-h LC50 doses, respectively, than those of T. japonicus. Chronic individual exposure to NH3−N concentrations over a specific threshold (≥ 0.2 mg/L for E. affinis and ≥ 14.6 mg/L for T. japonicus) affected survival rates, extended the duration of the nauplius and copepodite stages, and delayed maturation in both species. In contrast, batch culture showed that low concentrations of NH3−N were beneficial to the reproduction of T. japonicus, whereas such a trend was not clearly observed in E. affinis. Finally, we hypothesize that the differences in the NH3−N sensitivities of E. affinis and T. japonicus could be attributed to their evolutionary history in pelagic and benthic habitats, respectively. The low NH3−N tolerance of E. affinis indicates the importance of managing ammonia levels during their cultivation.