The capture and re-use of greenhouse fertigation water is an efficient use of fertilizer and limited water resources, although the practice is not without risk. Plant pathogens and chemical contaminants can build up over successive capture and re-use cycles; if not properly managed they can lead to reduced productivity or crop loss. There are numerous established and emerging water treatment technologies available to treat fertigation water. Electrochemical processes are emerging as effective means for controlling pathogens via in situ regenerative hypochlorination; a process that is demonstrated here to achieve pathogen control in fertigation solutions without leading to the accumulation of potentially phytotoxic free chlorine residuals associated with other chlorination processes. An electrochemical flow cell (EFC) outfitted with ruthenium dioxide (RuO2) dimensionally stable anodes (DSA) was characterized and evaluated for free chlorine production and Rhizoctonia solani inactivation in both irrigation and fertigation solutions. Pathogen inactivation was achieved at low current densities and short residence or cell contact times. Effluent free chlorine concentrations were significantly lower than commonly reported phytotoxic threshold values (approximately 2.5 mg/L) when fertilizer (containing ammonium) was present in the test solution; an effect attributable to reactions associated with breakpoint chlorination, including chloramine formation, as well as the presence of other oxidizable compounds in the fertilizer. Chloride concentrations were stable under the test conditions suggesting that the EFC was operating as a regenerative in situ electrochemical hypochlorination system. No significant changes to macronutrient concentrations were found following passage through the EFC.