"MCD and NDMC are directed to file a status report within 15 days after taking steps to desilt the drains so that the water-logging does not take place," a bench of justices S K Kaul and Vipin Sanghi said.
The court also asked the civic bodies and others to ensure that "the desilted materials are removed from the sites" and fixed the matter for further hearing on September 5.
The court's directions came during the hearing of a PIL filed by NGO Nyaya Bhoomi seeking steps to end the problem of water-logging in the capital.
The bench, meanwhile, allowed Gaurav Bansal, an advocate, to get himself impleaded as a co-petitioner to the PIL filed by the NGO.
Bansal, in his petition, had accused the civic agencies of doing "precious little" to prevent the recurrent malady before the monsoon.
The MCD and Public Works Department (PWD) have done nothing significant after 1998 to properly desilt drains, which was causing waterline on major roads even after the slightest of rain, the petition claimed.
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It also gave a list of 41 water logging-prone areas here.
Referring to a response received under the RTI, the petition said affected areas included Ashram Chowk, South Extension Part-I, DPS Road, Mathura Road, ISBT Kashmere Gate, RTR Marg near Moti Bagh flyover, Siri Fort Road, Dhaula Kuan underpass, and underpasses around Dwarka.