Thousands of dead fish have been seen since Thursday, they said.
People who had gone to the ghats for a bath were the first to spot them that day, an activist said.
Officials are also concerned as this has happened just ahead of Yam Dwitya on November 9 when a large number of devotees are expected for a holy dip in the Yamuna.
They said Haryana's irrigation department will probe how polluted water entered the Yamuna.
Meanwhile, in Agra, environment activists Sunday launched a big clean-up exercise on the riverbank opposite Etmauddaula monument, sometimes called the 'Baby Taj'.
Members of the River Connect Campaign were picking garbage, waste from leather units and damaged idols from the bank.
"The task is too big but citizens have to take the initiative. You can't wait indefinitely for government agencies to halt the pollution of our water bodies," said environmentalist Devashish Bhattacharya.
Each day thousands of tourists visit the monuments along Yamuna riverbanks but no one is concerned about keeping the environs clean," said another activist.
"People clean up their houses ahead of Diwali and dump the garbage in the river. This has to stop," she added.
Mathuradheesh temple priest Goswami Nandan Shrotriya said student groups should be involved in cleaning up the river which is not only the lifeline of the city, but the entire tourism industry is dependent on monuments along its banks.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)