The effect of fertilization on the physico-chemical water quality of six selected earthen fishponds in Ife North Local Government Area of Osun State was investigated for a period of two years sampling the ponds every other month. The fish ponds were grouped with regard to fertilization practice and water flowage regime into three sets comprising two non-flow-through ponds that received organic and inorganic fertilizers (FNF) two flow-through ponds that received the sameorganic and inorganic fertilizers (FF) and two unfertilized flow-through ponds. The investigated water quality parameters include water temperature, pH, transparency, dissolved oxygen, major ions, some plant nutrients and heavy metals using standard titrimetric and instrumental methods of analysis. The mean values of these parameters were not statistically different (p> 0.05) for the three sets of fishponds with the exception of sodium, Alkalinity, HCO3-, Conductivity and TDS which were each characterized with significant mean differences (p= 0.05) In general, the fertilized ponds were characterized by higher mean values in 24 of the 29 investigated water quality parameters than the non-fertilized ponds. Also the mean values of 22 out of the 29 investigated parameters were generally higher in the flow-through ponds than in the non-flow-through ponds. Increase in the parameters due to water flowage was statistically significant (p> 0.05) for sodium, alkalinity,bicarbonate, conductivity and TDS while the effect of fertilization was higher for the dissolved oxygen parameters, nutrients(NO3, PO4), major ions and apparent colour. Thus, the fertilized ponds were more saline (based on conductivity and TDS) better buffered and richer in nutrient than the unfertilized ponds. These effects were enhanced by flowage hence thefertilized flow-through ponds were characterised by the most suitable water quality for fish culture in the study-area whilethe fertilized non flow-through ponds was least suitable. The study revealed that to achieve the desired effect, pond fertilization must be accompanied by adequate water flowage especially in shallow fishponds.