Anaerobic digestion is an effective method for treating excessive submerged macrophytes, which are causing severe environmental issues worldwide. The biomethane potential (BMP) of submerged macrophytes varies depending on the seasonal changes in the lignin content of each species and the species composition of harvested submerged macrophytes. In this study, the seasonality of the chemical composition and BMP of three dominant submerged macrophytes species, i.e., Egeria densa, Elodea nuttallii, and Potamogeton maackianus, were elucidated. The theoretical monthly methane yield (TMMY) and theoretical annual methane yield (TAMY) of the submerged macrophytes harvested from Lake Biwa were then estimated. The methane yields of E. densa and E. nuttallii were 212–252 and 189–284 mL g-VS−1, respectively, while that of P. maackianus was lower, at 140–165 mL g-VS−1. Although chemical composition parameters, such as the lignin content, significantly changed between different seasons (p < 0.05), they range from only 7.8–14.6%. Therefore, the seasonal variations in the methane yield of the harvested submerged macrophytes depend on the species composition. The calculated TMMY of submerged macrophytes harvested from Lake Biwa was lower from autumn to spring (171–186 mL g-VS−1) than that in summer (213–231 mL g-VS−1) due to the predominance of P. maackianus. The estimated TAMYs for several years revealed that a constant volume of methane gas could be obtained annually from the harvested submerged macrophyte.