The death of Dr Deepak Amrapurkar, a gastroenterologist who worked with Bombay Hospital here, had caused widespread outrage.
Dadar police in central Mumbai yesterday arrested Siddhesh Bhelsekar, Rakesh Kadam, Nilesh Kadam and Dinesh Pawar, residents of a chawl in Parel area.
Probe found that they had opened the manhole so that the water in the area, which had entered their houses, could drain out, police said.
Dr Amrapurkar went missing after getting out of his car which was stuck in a traffic jam and walking home along a waterlogged street near the Elphinstone Road station on August 29, when torrential rains brought the city to a halt.
The four accused have been booked under section 304 (A) (causing death by negligence), said an officer from the Dadar police station, adding that further investigation was underway.
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