The students were being provided food and other supplies by the Indian-American community in the area.
India's Consul-General in Houston Anupam Ray has been in touch with the students and monitoring the evacuation process.
In New Delhi, External Affairs Minister Sushma Swaraj said two Indian students, Shalini and Nikhil Bhatia, have been admitted to the Intensive Care Unit (ICU).
"@CGHoust has informed me that 200 Indian students at University of Houston are marooned. They are surrounded by neck deep water," she tweeted.
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She said the MEA was ensuring that the relatives of the hospitalised students reach the health facility at the earliest.
"Mr Anupam Ray our CG (Consul General) Houston is organising the rescue operations," she tweeted.
Harvey, the most powerful hurricane to hit the US in 13 years, has left a trail of destruction as it swept through Texas after making landfall on Saturday, pummelling the region with heavy rains and claiming at least five lives.
Sewa International Houston - along with several other Indian-American community organisations - have teamed up to provide food and shelter to the affected people.
Major Indian organisations such as the India Cultural Centre, the India House, the Indo-American Charity Foundation and the Indo-American Political Action Committee have decided to coordinate their relief efforts through Sewa International.
Indian businesses and places of worship were providing shelter to displaced families. Indian restaurants were giving food packets to the people hit by the catastrophic flooding.