The Scottish Environment Protection Agency is Scotland's environmental regulator and national flood forecasting, flood warning and strategic flood risk management authority. Its main role is to protect and improve Scotland's environment. SEPA does this by helping business and industry to understand their environmental responsibilities, enabling customers to comply with legislation and good practice and to realise the economic benefits of good environmental practice. One of the ways SEPA does this is through the NetRegs environmental guidance service. It protects communities by regulating activities that can cause harmful pollution and by monitoring the quality of Scotland's air, land and water. The regulations it implements also cover the storage, transport and disposal of radioactive materials.

NatureScot is the operating name for the body formally called Scottish Natural Heritage. It is an executive non-departmental public body of the Scottish Government responsible for the country's natural heritage, especially its natural, genetic and scenic diversity. It advises the Scottish Government on nature conservation, and acts as a government agent in the delivery of conservation designations, i.e. national nature reserves, local nature reserves, national parks, Sites of Special Scientific Interest (SSSIs), Special Areas of Conservation, Special Protection Areas and the national scenic areas. It receives annual funding from the Government in the form of Grant in Aid to deliver Government priorities for the natural heritage.