The incident happened near the Bengali Ghat when Bhola and Gita - residents of Bharatpur district in Rajasthan - were taking the holy dip, SP City Shravan Kumar Singh said.
On Yam Dwiteeya, brothers and sisters taking bath together in the river is considered auspicious.
Nearly one lakh devotees come to Mathura annually to take the holy dip, but the incident has panicked them, said Vijai Bahadur Singh, PRO, Sri Krishna Janmasthan Seva Sansthan.
More than one lakh devotees took the holy dip in the river today, Mathura Municipal Commissioner Ujjwal Kumar said.
"After seeing the condition of the Yamuna, I had decided not to take the holy dip. However, my sister pressured me to take the bath," said Ram Khelari, who had come to the city from Gorakhpur.
Madhu Mangal Das, from Vadodara, who had traditionally carried the "holy water" with him, said he gave up the idea due to the pollition.
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