The management of water and the maintenance of its quality is the most crucial element in successful water gardening. A garden pond is an almost self-contained ecosystem which only interacts with the atmosphere for the exchange of gases such as oxygen and carbon dioxide. The toxic wastes that are released into the water have to be broken down otherwise they soon reach levels which are harmful to fish and other aquatic creatures. There is a naturally occurring process called the nitrogen cycle which copes with all this, although it is a wise precaution to monitor the levels of key chemicals regularly.

It depends upon the size of the pond, and also the temperature, as to how easy it is to maintain water quality naturally. Still water becomes thermally stratified during the heat of the day, because the sun's warmth is absorbed near the surface and cannot penetrate the depths. Small, shallow ponds may stratify when the day is warm, but return to a uniform temperature at night as the surface layers cool and mix with the lower layers. Such rapid changes can cause problems both with oxygen and the development of algal blooms.

With deep ponds changes are more likely to be seasonal than daily. In early spring a distinction develops between the warm upper layer and the cold layer near the floor of the pond. Between these layers there is a transitional zone. These all have an influence upon aquatic life, as the layers do not mix. The bottom layer at the pond floor receives no oxygen, but does benefit from organic debris which scatters into it from the upper layer. On the other hand, the uppermost layer receives none of the results of decay and by the end of the summer is nutrient deficient.

This can affect plants like floating aquatics which only live in that zone, one of the reasons why, in larger expanses of water, floating plants sometimes go into decline towards the end of the summer. These distinct zones remain until the turbulence created by fall winds mixes the various layers and they cool down.

With acidity and alkalinity, there can be considerable changes, depending upon the activities of pond life. In a pond, many chemicals dissolve into the water, and all these have an influence upon pH, which should ideally be monitored by periodic testing with a pH test kit. A pH value of between 7.0 and 8.0 is ideal for pond fish, although anywhere between 6.0 and 8.5 is acceptable. If the pH falls outside this range, pH adjusters should be used to stabilize it at a suitable level, and steps should be taken to find the cause.

One of the greatest influences upon pH can be the presence of algae, the pH value changing by as much as 3.0 between morning and evening. The reason for this is because algae uses carbon dioxide and removes carbonic acid from the water during the day, thereby raising the pH. At night algae ceases photosynthesising and produces carbonic acid, thus lowering the pH. So eliminating algae can have a considerable effect upon stabilizing pond acidity or alkalinity.