Plant viruses and viroids are transmitted in various ways, but transmission by water is especially interesting because it directly affects agricultural production. The research of plant viruses in environmental waters began in the 1980s and since then, methods of concentration and detection have evolved significantly. However, the “old” methods have been retained as complementary to the new ones. Today, HTS methods are increasingly used for virus detection and plant disease diagnoses. Plant viruses are usually not found free in waters, but in aggregates or adsorbed on solid materials. Plant viruses which are adsorbed to soil particles can retain their infectivity for a long period of time since the interaction with colloidal particles has a stabilizing effect on them. Some plant viruses can remain stable in water for a relatively long period of time, even up to several weeks. However, viroids, composed only of RNA molecules, can retain their infectivity for the longest time. Research efforts have been increasingly focused on the role of plant viruses in agriculture, and especially in the hydroponic systems that may have to replace fields in the future.