Seaweeds have been verified to effectively reduce the nutrients of aquaculture wastewater, and to increase the economic output when commercially valuable species are utilized. Pyropia/Porphyra/Neopyropia/Neoporphyra species are important seafood resources globally, and their growth and bioremediation capacities are affected by diverse biotic and abiotic stressors. In this study, we investigated the effects of desiccation (0, 1, 2, 4, and 6 h of air exposure), water velocity (0.1, 0.2, and 0.5 m s−1), and the nitrogen limitation period (1, 2, and 3 d) on the relative growth rates (RGR) and nutrient removal rates of Neoporphyrahaitanensis and Neoporphyradentata. The RGRs and NO3-N removal rates of the two species decreased significantly with increasing desiccation periods. A higher water velocity of 0.5 m s−1 had a greater negative impact on the RGRs and NO3-N and PO4-P removal rates than 0.1 and 0.2 m s−1. N. haitanensis exhibited a greater tolerance to water motion than N. dentata. Additionally, the RGRs and NO3-N and PO4-P removal rates were significantly different among the nitrogen limitation periods. N. haitanensis and N. dentata exhibited different nitrogen usage strategies after nitrogen limitation and recovery. These results provide valuable information relating to the excessive nutrient removal from aquaculture wastewater by Neoporphyra species.