This paper presents results of an aquatic vegetation resource potential assessment. The study is aimed at assessing the perspective of biotechnological approaches to reducing the biogenic pollution of water bodies by the removal of aquatic vegetation. The article analyzes the dominant species of aquatic vegetation in the Curonian Lagoon, and their productivity and resource potential. It was established that the concentrations of protein and fat in the biomass of four dominant plants are extremely low, making it impossible to speak of their values in terms of biomass processing. Based on elemental composition, we can conclude that the biomass of Phragmites australis should have a high calorie content because it has a high carbon and hydrogen content (49.6% and 7.1%, respectively), resulting in a high energy value. Synchronous thermal analysis revealed that the maximum energy values of biomasses of Phragmites australis and Scirpus lacustris have a net calorific value of 12.62 and 12.55 MJ/kg, respectively. At the same time, the biomass of these plants has a low ash content (around 6.6–7.6%) and a low sulfur content (less than 0.41%). An analysis of the composition of aquatic vegetation biomass samples allowed us to establish that, given the permissible collection time (no earlier than September), the search for directions in the utilization of aquatic vegetation should focus on processing cellulose with the production of crystalline cellulose, biochar, or biofuel via anaerobic digestion. The removal of the excess biomass of aquatic vegetation (Phragmites australis) will allow the reduction of the nitrogen and phosphorus load in the water body by 140 kg/ha and 14 kg/ha, respectively.