Modification of Indus River flows to meet anthropogenic needs has seriously undermined the ecological benefits the river generates in the deltaic region. This paper provides an assessment of ecological conditions of the Indus Delta under different climate change scenarios by using ecological health of the Indus River as a proxy. First, we assessed the existing state of deltaic ecology and categorised it into an arbitrary environmental management class (EMC). Then, using Global Environmental Flow Calculator, we determined the Environmental Flows (E-flows) that are required for the Indus delta in (i) the present, and (ii) in the future under two climate change scenarios. Our analysis shows that due to inadequate and inconsistent release of E-flows downstream of Kotri barrage, deltaic ecosystems have deteriorated overtime. Our analysis reveals that under climate change Scenario 1, more flows may be available that can bring river flows close to natural E-flows. Under Scenario 2, there may be reduced river flows to the extent that E-flows required under prevailing conditions would not be possible. The study concludes that if the current deterioration of aquatic ecology continues, it will be challenging to maintain present, or achieve higher ecological management class (EMC), regardless of the changes in river flows in the future. In this light, there is a need to interlink economic and development needs of communities with environmental needs of Indus River in the deltaic region. Most importantly, there is a need for ensuring climate-compatible e-flows in water regulating sites such as Kotri Barrage.