Phenolic acids—excreted both as root exudates and by microorganisms—are of interest in cultivation systems of different horticultural crops since they have been claimed to accumulate in closed hydroponic growing systems. The aim of the present investigation was to assess the phytotoxic effects when hydroponically grown tomato plants are exposed to phenolic acids in the root environment. The tomato plants were grown in static aerated culture and exposed to benzoic, caffeic, chlorogenic, ferulic, p-hydroxybenzoic, salicylic and vanillic acid at concentrations of 50, 100, 150, 200 and 400μM in the fresh nutrient solution. The highest concentration of all tested compounds significantly reduced fresh and dry weights. Salicylic and ferulic acid affected plants already at 150 and 200μM while effects were less pronounced for p-hydroxybenzoic and chlorogenic acid. Chlorophyll fluorescence analysis did not result in any significant difference between any of the tested acids or concentrations. No clear dose-related pattern was obtained with respect to number of leaves and plant length. Visual assessment showed that the most deleterious effects appeared on the roots, which were discoloured and/or had slimy coatings when exposed to the phenolic acids. The uptake of several mineral nutrients was influenced at the highest concentration of all studied compounds. Significantly more bacteria were enumerated in the nutrient solution treated with phenolic acids compared to the controls. Most of the phenolic acids were degraded after 2 days during the start of the trial and within 1 day at the end of the trial. Concentrations phytotoxic to small tomato plants were 1000-fold higher than the natural concentrations measured before. Instead of potentially harmful, the relevance of certain phenolic acids as antimicrobial substances should be considered.