The objectives of this study were to evaluate the risks and benefits of using artificial wetland-treated waters to irrigate tomato plants (Lycopersicom esculentum) and the potential for suppression of Pythium ultimum. The experiment was conducted in a greenhouse using tap water (control) and treated waters coming from three types of horizontal subsurface flow artificial wetlands filled with pozzolana and implanted with common cattail (Typha latifolia). Wetland units contained either a simple [artificial wetland with sucrose (AWS)] or complex [artificial wetland with compost (AWC)] carbon source or no [artificial wetland with no carbon (AW)] additional carbon source. A complete randomized split-block design comparing root sensitivity to root rot (inoculated and uninoculated plants) in main plots and four nutrient solutions [1) control, 2) treated water from AWS, 3) treated water from AWC, and 4) treated water from AW] in subplots was used in six replications. Tomato plants were inoculated with P. ultimum twice during the experimental period. The use of treated waters reduced the in vivo root Pythium population by 84% and 100% when the treated waters were from AWS and AWC, respectively. In vitro trials showed that sterilization or membrane filtration (0.2 μm) of treated waters significantly reduced the potential for suppression of P. ultimum, suggesting that microbial activity played an important role. On the other hand, all AW-treated waters had a negative effect on root development of uninoculated young tomato plants. Root dry weights of plants irrigated with treated waters was 56% lower than in control plants, while their shoot:root ratio was two times higher for plants irrigated with treated waters. The inoculated and AWC-treated water treatments also reduced the Fv:Fm ratio of dark-adapted leaves, representing the maximum quantum efficiency of photosystem II. Organic compounds present in treated waters, expressed as total and dissolved organic compounds, may have affected tomato root development.