Fungal and Oomycete plant diseases cause economically important losses in soilless cultures by affecting both yield and quality of productions. In these systems, the irrigation water is the main source of introduction of pathogenic microorganisms whose spreading is enhanced by the recycling of the nutrient solution, increasing thus the risk of root disease. To control the disease development, a chemical treatment through chlorination of water supplies was used in this study. The present experiment was conducted over a period of three years during which water and root samples were collected yearly in 8 to 13 tomato soilless greenhouses (8 greenhouses in year 1 and 13 in years 2 and 3). In control storage tanks, the water added to the nutrient solutions was frequently contaminated by Pythium spp. Contamination rates ranged from 5 to 30 Pythium cfu L-1 but were reduced to 0 to 3 cfu L-1 after the chlorination treatment of the water. However, these contamination levels were lower than those detected in the flowing nutrient solution samples: around 50 to 150 Pythium cfu L-1. During winter, roots of tomato plants in control conditions were weakly colonized by Pythium spp. (below 50 cfu g-1 of roots). These values dramatically increased during spring and summer; around 200 and 600 to 800 cfu were respectively detected per gram of roots. No root colonization by Pythium spp. was detected in winter after the chlorination treatment in the solutions; the colonization level reached around 50 cfu g-1 of roots in spring and 150 to 200 cfu g-1 of roots in summer. In conclusion, the chlorination treatment experienced here has been shown to be effective for the disinfection in the solutions and to have a key impact in reducing and delaying the root colonization by Pythium spp. Nevertheless, this treatment has the disadvantage of eliminating not only harmful but also beneficial indigenous microorganisms.