This experiment was conducted by employing immobilized microorganisms (I) on ceramics and Myriophyllum aquaticum (M) and unloaded ceramsite (UC) to purify aquaculture wastewater in the lab. Different nitrogen forms removed from aquaculture wastewater and the dynamic distribution of four groups of bacteria involved in nitrogen cycling, ammonifiers (AB), nitrosobacteria (NOB), nitrifiers (NB) and denitrifiers (DB), were evaluated. Our results revealed that the removal efficiency of nitrogen and chemical oxygen demand (COD_Mn) performed by the combined treatment (I+M) was significantly higher than when used separately (P<0.05). By the end of day 15, the nitrite and ammonium removal rate by the I+M treatment reached 50.83% and 62.38 %, respectively, significantly higher than I (39.55% and 51.17%) or M (40.78% and 53.31%) separately (P<0.05). At the end of the experiment, COD_Mn removal by the I+M treatment was significantly higher (67.23%) than that of treatment I (48.23%) or M (33.35%) (P<0.05); the nitrate removal rate (88.74%) was also significantly higher than I (67.85%), but there was a significant difference between I+M and M (P<0.05). In addition, four groups of bacteria on the roots surface increased in certain extent compared with treatment M, and during the last period four groups of bacteria on the ceramic surfaces showed an overall downward trend, e.g. AB in treatment I+M were 1.8~2.6 magnitudes lower than in treatment I. Principal response curve analysis (PRC) showed that turbidity, -N, TN contribute great to total difference, during the early and middle stages of this experiment the combined treatment was more efficient at removing nitrogen than treatment I or M, but the overall differences between I and UC decreased greatly in the later stage with differences between I+M and I becoming small. This purifying method has some drawbacks and therefore requires further optimization to ensure its effects are long lasting.