A seven-month research evaluated the management effect on the water quality and sediment of seven fish ponds. Water and sediment were collected at nine sample sites: seven in the fish ponds; one in inlet water and another in the fish farm’s effluent. The soil samples were analyzed for macro- and micro-nutrients and the water samples were analyzed for physical and chemical parameters. Management and local climate conditions affected nutrient seasonality in the sediment and featured high concentrations of Al, Ca, Cu, K, Mg, C, Na, Zn and OM at the effluent with low pH, ranging between 4.4 and 6.5. Sudden decrease of DO (less than 3 mg/L) during the rainy season, with a 180 mmrainfall, and a TSS increase (approximately 10 mg/L) were reported. Use of organic manure in fish pond V₆ caused higher rates of ammonia (over 1 mg/L). Due to the sediment’s acid pH (less than 4.8) and Al at 0.92 mg/L at the effluent, great care was required in the fish farm. Maintenance and procedures management in the fish farm under analysis should be given more attention since high levels of Al, Fe and acid pH and low levels of potassium and phosphorus in the sediment may produce unfavorable conditions in the water column, and may ultimately have an impact on fish.