Raising awareness of adequate biofuel production today is of exceptional importance for the future environmental and economic perspective. In addition to the production itself, it is extremely important to improve the existing ones and to design new favorable biofuel production processes that do not require large investments or further pollution of the environment. Today, there is more and more talk about third-generation biofuels, namely biofuels produced from algae, which are known to have a noticeably smaller impact on the environment and its aspects through their production. As an example of such a fuel we can take biodiesel produced from the lipid microalgae, such biodiesel is preceded by the processes of microalgae production, extraction of microalgae and drying, the breaking of cells and the extraction of lipids and their transesterification. Each of the individual processes can have a negative impact on the environment if it is not carried out responsibly and adequately. When producing biofuels, it is necessary to pay attention to the choice of microalgae, the appropriate nutrient base, potential bioractory systems, process management conditions and biomass extraction methods and lipid purification. When producing, it is necessary to constantly monitor changes in the ecosystem. We know that algae are indicators of the state of the environment and are the first to react when disrupting ecosystems. One of their reactions is the appearance of mass algae blooms during a change in weather conditions or an increased inflow of nutrients. In this thesis I tried to present in more detail the importance of the use of biomass and biofuels over fossil fuels, the importance of algae and the very impact on the environment of biofuels production from algae.