Under the current scenario of diminishing Indus River flows and changing the climate, the Indus Delta, the world’s 5th largest delta which has undergone rapid changes in water bodies and vegetative cover since last few decades, is under serious risk of losing its ecological functions. Assessing the temporal variation in vegetative cover and water bodies of the Indus Delta is essential for the future planning and ecosystem management in this region. The present study quantified the temporal patterns of the surface water bodies and vegetation cover, including crops, mangroves and other natural vegetation in the Indus Delta, by using field survey and remote sensing technique during the last 27 years. Results showed that the area covered by vegetation declined from 3002.35 km2 (22.98% of the entire delta) to 2817.03 km2 (21.56%) from 1990 to 2017, within which the area covered by mangrove forests declined from 1032.49 km2 (7.90%) to 812.55 km2 (6.22%). However, the area of water bodies increased from 1611.67 km2 (12.39%) to 3007.15 km2 (23.8%) in the same period. The reduction in freshwater flow to the delta, surface and subsurface seawater intrusion from the Arabian Sea and irrigation waters are the potential causes. The study would be helpful for policymakers to mitigate negative impacts and protect the ecosystem of the Indus Delta.