Selecting the source of water used in an aquaponics system can greatly influence the water quality, and is an important first consideration. Potential sources include well water, municipal water, and surface water. Surface water is not recommended because of the difficulty in ensuring consistency in water quality due to risk of contamination. Municipal water is treated with chlorine and chloramines, which must be removed before it can be used. Whatever source of water is used, it is very important to have it tested and to obtain a water quality profile to ensure that it meets the requirements to grow fish and plants.

Testing frequency will vary depending on the parameter being monitored. However, as a general rule, start-up systems should be tested daily so that adjustments can be made quickly when needed. For example, in response to high ammonia levels, feeding levels can be reduced, aeration can be increased, or water can be diluted. Once nutrient cycles are balanced, weekly testing is usually sufficient.

In all cases, it is important to record all parameters such as pH, Hardness, Alkalinity, Temperature, and all nutrients such as Nitrogen, potassium, calcium, Magnesium, Phosphorus and Sulphur. Keeping good records of your water quality measurements can help greatly in observing trends and diagnosing future problems.

Maintaining a balance between water quality conditions that are optimal for fish, nitrifying bacteria, and plants is crucial to a healthy and productive aquaponics system. These are simply guidelines to inform growers of optimal conditions to help them make better decisions on how to manage a healthy, functioning system.