Environmental characteristics of the coral reef-seagrass ecosystem of selected Lakshadweep Islands (India) were assessed with a view to understanding the future climate change scenario in the region. Images obtained from the Indian remote sensing satellite (IRS P6) were used to identify the different zones such as the corals, the seagrass and the sandy region. The pH (7.6–8.6) of sediment was relatively high in the coral reef compared to the seagrass area, possibly indicating a climate shift-induced coral bleaching. The water quality and sediment texture generally showed marked intra- and inter-island variations illustrating that these coral reef ecosystems are highly vulnerable to climate change brought about by increased human interventions. Future research should therefore explore the habitat and resource connections, to predict their restoring capabilities for a sustainable exploitation. With an alarming increase in the population and associated developmental activities, the island ecosystems are expected to respond severely to the climate change, which may eventually lead to mass mortality of corals due to bleaching.