This study established wetland microcosms that were either unplanted or planted in monoculture with native mangrove species in Taiwan (Avicennia marina, Rhizophora stylosa, and Lumnitzera racemosa) for the purpose of receiving high-salinity mariculture effluents; additionally, the microcosms operated at different hydraulic retention times (HRTs). Plant growth and the performance of the microcosms with respect to pollutant removal were investigated. The results showed that seedlings of all three mangrove species survived and grew sufficiently well under continuous flooding. The presence of mangroves consistently improved SS, BOD5, and TP removal, particularly under short HRT conditions. The mangrove microcosms removed pollutants from the mariculture effluents with efficiencies of 5.7–27.1% (SS), 4.9–36.3% (BOD5), 18.7–29.9% (TP), 21.2–49.8% (NH4-N), and 5.4–37.7% (NOx-N). A. marina and L. racemosa were more tolerant of continuous flooding than R. stylosa. However, no species displayed consistently superior performance in decreasing all pollutant-related parameters investigated. For all pollutants, microcosms operating at a 2-d HRT exhibited a higher removal efficiency than those operating at a 0.5-d HRT.