In this study, eight different submerged aquatic species were screened by batch biochemical methane potential and anaerobic degradability tests to identify a promising/suitable feedstock. Kinetics of the best-screened substrate were studied in a mesophilic semi-continuous experiment. The aquatic species Myriophyllum aquaticum, Egeria densa and Potamogeton perfoliatus showed relatively higher methane yields of over 400 NmL/g-VS (volatile solids). Semi-continuous operation was carried out by feeding E. densa for over 400 days. The achieved results were 33%–53% chemical oxygen demand (COD) reduction and methane yield of 126–231 NmL/g-VS with a short hydraulic retention time (HRT). Additionally, the NH4+ and PO43− releases from the biomass to water were found to be low (18%–27% and 2.5%–3.9%) throughout the experiment. Hydrolysis was the limiting step in the digestion of E. densa, regardless of changes in HRT (15–45 days). The acid-phase model indicated that the hydrolysis rate constant (kh) of E. densa was 0.058 one/day, which was one third lower the kh value of food waste, but quite similar to cow manure.