In order to study the effect of aeration on vertical distribution of the ions in overlying and interstitial waters in aquaculture systems, we constructed 8 plexiglass microcosms paved with aquaculture sediment, including 4 tests with continuous aeration and 4 controls without aeration. Intact overlying and interstitial waters were collected by Peeper (pore water equilibriums) devices on the days of 0, 1, 4 and 7 respectively, before and after initiating the aeration. The ions of NH₄⁺-N, NO₃^--N, NO₂^--N, PO₄^3--P and SO₄^2--S were measured by miniaturized photometrical methods using a microplate reader. The result showed that one week aeration didn’t significantly change the vertical distribution of NH₄⁺-N in interstitial and overlying waters, but it greatly increased the concentration of NO₃^--N in overlying and 0–2 cm interstitial waters. The highest average concentration of NO₂^--N presented in surface layer waters before the aeration, while it peaked in the surface sediment interstitial waters at the depth of 1 cm during the aeration. The aeration promoted the adsorption and immobilization of PO₄^3--P in the sediment, greatly decreased the concentration of PO₄^3--P in overlying and 0–2 cm interstitial waters. The concentration of SO₄^2--S in overlying and 0–2 cm interstitial waters was significantly increased by oxidizing reducible sulfur in biological and chemical path. The physicochemical property of the overlying water on 1 d, 4 d, 7 d was greatly changed, which distanced farthest away from the control group, suited at the bottom of the PCA image. On the contrary, it didn’t distinctively chang the property of the sediment interstitial waters, which suited at the left site of the PCA image. In conclusion, aeration conditions can elevate oxidative ions of NO₃^--N, NO₂^--N and SO₄^2--S, and reduce the ions of PO₄^3--P which can cause eutrophication. It greatly changes the physicochemical property of the overlying water and surface sediment interstitial waters, which is an applicable method to control aquaculture pond water quality and remediate sediment.