Aquatic plants, overgrown in the southern basin of Lake Biwa, have potential for biomass resources to generate biogas by methane fermentation. The liquid residue (digestate) generated abundantly during methane fermentation process contains plenty of plant nutrients. In this study, the fertilizer properties of this digestate were investigated by hydroponic production of leaf lettuce and Japanese mustard spinach to evaluate the applicability of digestate in hydroponics. Ammonium (NH4-N), contained originally in the digestate at high concentrations, was reduced to about 0.3% of original and converted to nitrate (NO3-N) by biological nitrification. When cultivated using nitrified digestate diluent supplemented with Fe-EDTA to suppress Fe deficiency, the growth of two species was significantly promoted as compared to when cultivated without nitrification and/or Fe-EDTA supplementation. On the other hand, as a result of extremely high Mn concentrations in the digestate, Japanese mustard spinach plants remarkably exhibited Mn toxicity symptoms during cultivation. Aquatic plant-derived digestate seems to be utilized in hydroponics as a nutrient solution by nitrification and only adequate dilution except for Fe-EDTA supplementation, but risk for excess Mn toxicity, which is probably caused by the contamination of Brazilian waterweed to fermentation substrate, should be noted.