Most diseases for plants are from fungus, bacteria and virus.
Many diseases are soil born, and they appear in hydroponic systems in contaminated media.
There are several ways of ensuring media is clean. One is to use new media. Another is to sterilize the media by drying well in the sun, or using a sterilizing solution such as copper sulfate. In most cases in hydroponics, the media can be sterilized with sun drying and heat. Any sterilizing solutions may cause problems if it leaves any residue in the media.