A 155-day experiment was conducted in land-based enclosures to examine the effects of three fertilization programs on chemical water quality for integrated culture of freshwater pearl mussel Hyriopsis cumingii and fish. The pearl mussel was co-cultured with grass carp, gibel carp, silver carp and bighead carp, and the stocking ratio of fish to mussel was 1.5:1. Three fertilization programs, including fertilizing with duck manure (DM), with chemical fertilizer (CF), and with duck manure and chemical fertilizer in combination (DC), were examined. The results showed that there were no significant differences in the SD and concentration of dissolved oxygen (DO), SO42-, Cl-, CO32-, HCO3-, Ca2 , Mg2 , hardness, alkalinity, ammonia (TAN), NO3-N, NO2-N, PO4-P, total nitrogen (TN), total phosphorus (TP) and chemical oxygen demand (CODMn) between the fertilization treatments. The ratio of PO4-P to TP was higher in the CF enclosures than in the DM enclosures. The pH was lower in the CF enclosures than in the DM enclosures during the earlier phase (from May 20 to July 18). With the progress of the experiment, the SD, concentration of DO and Ca2 , and ratio of Ca2 to Mg2 decreased, while the concentration of TAN, NO2-N, TN, TP and CODMn increased. The results of this study indicate that using different fertilization programs had no significantly different effects on the major ions, hardness, alkalinity, TAN, NO3-N, NO2-N, PO4-P, TN, TP and CODMn in the enclosures with integrated culture of freshwater pearl mussel with fish and fed formulated fish feed intensively. However, the concentration of CODMn was lower, but the ratio of PO4-P to TP was higher, in the enclosures fertilized with chemical fertilizer than in the enclosures fertilized with duck manure. The concentration of CODMn and ratio of PO4-P to TP were at median levels in the enclosures fertilized with chemical fertilizers and duck manure in combination. The higher growth rate and nacre secretion of H. cumingii hung in the enclosures supplied with both chemical fertilizers and duck manure suggests the water chemistry parameters in these enclosures are suitable for H. cumingii farming.