The research was focused on the identification of interactions between hypochlorite used as a disinfectant for a recirculating tomato production system and the spread of microorganisms, plant characteristics and fruit quality. Potassium hypochlorite (1% KCLO) supplemented once a week for 90 min into different nutrient solution ranks until a free chlorine concentration of 1 mg L-1 (DI) and 2 mg L-1 (DII) caused benefits but also hazards. Results showed that microorganisms were suppressed by up to 100%. Plants exposed to treatment DI showed a comparable plant height in comparison to control plants, whereas this plant parameter was significantly increased by 12 cm caused by treatment DII after a growing period of seven weeks. However, the formation of leaves was more pronounced by treatment DI. This was obviously the main reason for an increase in yield by 10% (DI) calculated in comparison to control plants. While phytotoxic problems can be excluded, the chlorate (ClO3-) content in tomatoes increased from 0.01 mg (control) to 0.22 mg (DI) and 0.25 mg (DII) ClO3- kg-1 fresh weight. This enhancement should be seen as critical value because new maximum residue levels (MRL) will be defined next year. The levels of lycopene increased with increasing concentrations of hypochlorite as well, which was probably based on a stress response owing to the accumulation of chlorate. Apart from the ClO3- accumulations in fruit, treatment DI represents the most promising disinfection for recirculating tomato production systems.