The effect of aquacultural practices on the bottom sediment quality of six selected earthen fishponds in Ife North Local Government Area of Osun State was investigated for a period of two years. The fishponds were grouped with regard to fertilization practice and water flowage regime into three sets comprising two fertilized non-flow-through ponds (FNF); two fertilized flow-through ponds (FF) and two unfertilized flow-through ponds (NFF). The investigated sediment quality parameters include color and textural composition, salinity parameters, major ions, organic parameters and heavy metals using standard methods. The parameters were not statistically different (P > 0.05) for the three sets of fishponds with the exception of calcium which was significantly available in the fertilized flow-through pond. The fertilized ponds were however richer in nutrient and of better drainage quality than the unfertilized ponds. The parameters with higher mean in the fertilized ponds (FNF and FF) were 16% higher on average and flow-affected parameters were 67% higher on average in the flow-through ponds (FF and NFF), of which 7.00-fold higher lead concentration contributed most to this situation. Of these parameters, cations, anions, micronutrients were found to be of highest mean concentration in fertilized flow-through ponds. However, the presence of significant levels of calcium ions as well as minimal accumulation of clay, silt and nutrients in fertilized flow ponds made this fish culture method most suitable.