Intact overlying water and interstitial water in sediments were collected by Peeper devices from intensive hybrid snakehead (Channa maculata♀×C. argus♂) aquaculture enclosures in Nansha District, Guangzhou. The concentration of NH₄⁺-N, NO₃^--N, NO₂^--N, PO₄^3--P, SO₄^2--S and Fe²⁺ were measured by miniaturised photometrical method using a microplate reader. All measured ions showed strong vertical distribution patterns, and the depth related samples were divided into three groups, overlying water group, surface layer sediment group (water-sediment interface group) and lower layer sediment group with distinct differences. Diffusion fluxes of the ions were calculated by the Fick's First Law. NH₄⁺-N, NO₂^--N, PO₄^3--P and Fe²⁺ were released from the sediment to overlying water, while NO₃^--N and SO₄^2--S in the overlying water were absorbed into the sediment. Among them, NH₄⁺-N and SO₄^2--S have much higher exchange fluxes than the other ions relatively. And NH₄⁺-N was the main endogenous pollution ions in the hybrid snakehead aquaculture enclosures with the diffusion fluxes of 76.432, 111.631 and 209.835 mg/(m²·d) respectively.