The Velvet Revolution occured in the late 1989 has given fundamental changes politically, economically, and socio-culturally to the Czech Republic. The communist regime which had been ruling since World War ll was terminated and replaced by a democratic political system. This period was highlighted by mass demonstration which prosecuted the government to give more attention on environmental aspects in the development of the country. Based on some research, it was found that since 1980s, environmental condition in the Czech Republic (Czechoslovakia before) was very horrendous and due to this, the Czech Republic became one of the high polluted countries in Europe. Meanwhile, efforts to save the environment were hindered by communist regime which did not allow people to express their aspirations. Nevertheless, environmental movement in the Czech Republic has been emerging since the communist regime was in power. By using qualitative approach and indepth interview to collect primary data and literature study as secondary data, this research is conducted to understand the process and the development of independent organizations (NGOs) which concern with environmental problems since the post Velvet revolution period until today. This research also try to identify the role of NGOs and their problems in facing negotiation with the government and strategy of the Czech government in dealing with the European Union challenges.