Backwaters in Kerala state of India are water bodies nourished by rivers but there is little or no water current and in most cases connected to the sea. Vembanadu lake, the largest backwater in the state is also the largest wetland system in South India. The major attraction of the area is backwater tourism and is emerging as the main income source of the region since the introduction of houseboats. Vembanadu lake is included in the Ramsar sites and there is a great concern on the environmental degradation due to the backwater tourism. Hence a study was taken up to assess the ecological threats to the backwaters due to pollution. It was found that pollution from untreated sewage waste, seepage of oil from engine driven boats, discharge of non-biodegradable wastes were serious issues. Possibilities to use green energy technologies such as bioenergy and solar energy were evident in the study.