This study aims to find out (1) the role of the Magetan Regency Environment Agency in preventing B3 waste pollution of the tanning industry in the Gandong River, and (2) the factors that hinder the Magetan Regency Environment Agency in carrying out its role to prevent pollution of Gandong river flow. The principle of regional autonomy adopted in the system of government gives each region the authority to regulate its government affairs in this case is the protection and management of the environment independently. The Magetan Regency Environment Agency is an institution authorized by the Regent of Magetan to conduct environmental protection and management activities in Magetan Regency. Based on the results of research and discussion, researchers concluded that: First, one of the activities of environmental management implementation carried out by the Environment Agency of Magetan Regency is to conduct supervision to prevent the occurrence of B3 waste pollution. The form of supervision carried out is to include administrative supervision, namely the examination of environmental documents and permits owned and also technical supervision carried out by the Leather Industry technical implementation Unit (UPT) and Leather Production in organizing the WWTP/IPAL. In conducting supervision on the prevention of liquid waste pollution, the parameters used by the Environment Agency is Law No. 32 of 2009 on Environmental Protection and Management mentioning that pollution control and environmental damage are carried out with several measures, namely prevention, control/countermeasures and coaching/recovery. Second, the Environment Agency of Magetan Regency in preventing pollution has been running in accordance with the legislation but there are some obstacles including the river capacity factor that has been decreased in quality so the river pollution easily occurs, factors of lack of competent human resources in environmental management, lack of awareness and community participation of business actors in participating in the program of counseling/ coaching activities on preventing environmental pollution of the river flow, lack of response from industry players them selves in response to the letter of reprimand that has been given, so that it can not be realized appeals, proposals, and suggestions that have been given by the Environment Agency.