This study focuses on the post effect of flooding on soil quality parameters in agricultural farmlands in Nigeria. Soil samples were collected from farmland in Alihame Agbor, Ika South local government area of Delta state, Okwei in Asaba, Oshimil South local government area of Delta state and fegge in Onitsha South local government area of Anambra state. Farmlands in Asaba and Onitsha were used for the post flooding study, while farmland in Agbor served as control since it was not affected by flooding. Soil physicochemical parameters such as pH, electrical conductivity, total organic carbon, total organic matter, total nitrogen, total phosphorus, cation exchange capacity, moisture content and metals (Cd, Pb, Cu, Mn, Ni and K) which were used as index for assessing the effect of flooding on soil quality were analyzed using standard methods. Significant effect of flooding was observed on soil properties on the flood affected farmlands when compared to the control farmland, which was statistically justified at 95% confidence limit (p ≤ 0.05). There were considerable decreases ranging from 4% to 53% at p ≤ 0.05 in the values of pH, total organic carbon, total organic matter, total nitrogen, total phosphorus and cation exchange capacity on the flood affected farmlands when compared to the control farmland; except for electrical conductivity where an increase of 54% and 92% at the flood affected farmlands in Asaba and Onitsha respectively was observed when compared to the control. Higher moisture contents were also recorded of up to about 17% and 45% at the flood affected farmlands in Asaba and Onitsha respectively, when compared to the control. Reduced concentrations ranging from 25% to 49% of essential micronutrients such as Mn, Ni and K were observed on the flood affected farmlands, reflecting the negative impact of the flood. Undesirable effect of the flood was also observed in the flood affected farmlands when compared to the control farmland as increased concentrations ranging from 18% to 114% of Cd, Pb, and Cu, were recorded. The findings of this study revealed significant impacts of the resulting flood on soil quality of the affected farmlands with major attendant effect of the flood felt on farmland in Asaba. As a consequence, measures should be put in place by government and concerned agencies to avoid future flooding of farmlands so as not to further expose the natural quality of these farmlands to the degradative and devastating effect of such flooding.