Hydrogen peroxide has been used as a sanitation agent for many years. Recently, hydrogen peroxide products have been used to remove algae from irrigation lines and sanitize hydroponic systems between uses. However, hydrogen peroxide can have phytotoxic effects on plants at high concentrations. The goal of this research was to determine if hydrogen peroxide treatments affected plant and algae growth in the ebb and flow hydroponic systems. The research was conducted at the Department of Horticulture and Landscape Architecture greenhouses in Stillwater, OK. Two cultivars of lettuce, ‘Green Forest’ and ‘Tropicana’, and two cultivars of basil, ‘Aroma II’ and ‘Genovese’, were transplanted into the ebb and flow hydroponic systems, and three different hydrogen peroxide products, PERpose Plus, ZeroTol, and 3% hydrogen peroxide, were applied at different rates and combinations in two experiments. Shoot fresh weight in lettuce was found to be significantly greater in control and 3% hydrogen peroxide treatments for both cultivars; however, in ‘Tropicana’ those treatments were not different from any other treatment. Greater amounts of PERpose Plus and ZeroTol, such as 60 mL, restricted plant growth in lettuce, whereas only cultivar differences for SPAD and plant width were reported for basil. Algae growth was not significantly controlled by any treatment in this research based on algae counts, weights, or spectrometer readings. However, algae species quantification did show that Microspora tumidula was found in the greatest concentrations in control, with a 96.0%, 99.2%, 94.0%, and 97.9% reduction in the 15 mL ZeroTol, 60 mL ZeroTol, 15 mL PERpose Plus, and 3% hydrogen peroxide treatments, respectively. Other algae genera identified included Scenedesmus, Chlamydomonas, Gloeocystis, Tetraspora, Leptolyngbya, Pennate diatoms, and Centric diatoms.