The pythium fungus is one of the serious diseases that growers can encounter in hydroponic systems. The disease can be kept at bay if the irrigation system can be closed of from the environment. The best method to control pythium and phytophtera is by maintaining a 2.5% concentration of hydrogen peroxide. It has been determined that pythium and phytophtera infestations increase radically with increasing temperatures. Any temperature above 22°C will create an ideal environment for the fungus to develop.

Maintaining the correct nutrient concentrations at all times can also help in reducing the occurrence of these funguses. It has been found that adequate manganese concentrations can contain plants to pythium infection. Copper can also be used to suppress microbial growth but high Cu levels are toxic to plants.

The flow rate of the water can also help in reducing the occurrence of funguses. Low flow rates increases the risk that the spores can attach themselves to various particles in the irrigation system and spread. By increasing the flow rate of the solution the risk is minimized. The flow rate can be increased by increasing the angle in which the channels are laid as well as increase the stone (gravel) size up to 13mm.

Sanitation is important in controlling various diseases. It is important that paths and roads should not be made of soil that creates dust during dry seasons. Dust particles contain many bacteria and spores that can create diseases. Planting grass around the growing areas and covering the roads with either tar or gravel will greatly reduce the chance of fungus infections.