The decline of fossil fuels, the increase of greenhouse gases and the global demand for energy are driving the search for alternative energy sources. Anaerobic digestion is a promising technology because it can convert organic biomass into biogas. As the climate warms, there is an increase in biomass of plant origin in water bodies, and ecosystems are unable to clean themselves. This work aims to show that macroalgae and aquatic plants can be an excellent raw material for biogas production. By mixing them with co-substrates such as cattle manure, higher biogas and methane yields can be obtained. When Cladophora glomerata and Zostera marina macroalgae are mixed with cattle manure, the biogas yield is up to 458.8 mL/gVS and 397.9 mL/gVS, respectively. Methane concentration remained high and reached 62.4%–64.1%. The obtained research results show the high energy value of biogas and the energy potential of biomass. Macroalgae increased the energy potential of biogas to 22.9 MJ/m3, and the energy potential of biomass reached 2.40 MJ/Kg. Due to its high energy value, biogas produced from the considered substrates can be an excellent alter-native to fossil fuels. Integrating aquatic macroalgae into anaerobic digestion is a promising approach for a waste-free marine and freshwater system.