Ganguly said in his resignation letter that he stepped down to "obviate any further controversy" and "to ensure the peace and happiness" of his family.
He said during his tenure as the WBHRC head, the number of complaints lodged doubled due to the confidence people had in the commission's working.
"We have been able to earn the trust of the people. The number of complaints from 5,000 rose to 12,000- 14,000 complaints now which is likely to grow. But while doing this, I could feel the state government did not like this," he told a TV channel ABP Ananda.
Ganguly was under growing pressure to resign from the post following allegations of sexual assault levelled by a law intern against him.
He resigned Monday, hours after the Supreme Court dismissed a petition seeking to restrain the government from proceeding against him. Ganguly, however, claimed he had "nothing to do" with the Public Interest Litigation.
The union cabinet had already cleared the home ministry's proposal for a presidential reference to the Supreme Court for a probe into the allegations of sexual assault against him.
As the chairperson, Ganguly ordered the state government to pay compensation to Jadavpur University professor Ambikesh Mahapatra and his neighbour who were arrested for circulating emails mocking Banerjee.
Ganguly was under growing pressure to resign.
WBHRC also directed the government to pay compensation to a farmer who was dubbed by the chief minister as a Maoist and arrested by police after the farmer asked her about the rising price of fertiliser at a public rally.
"I still remember when the commission made the recommendation on Ambikesh, the very next day, the Chief Minister Mamata Banerjee, without naming, spell out her anguish against me in the state Assembly," Ganguly said.
"She had said, 'I brought in an impartial man, but the way he is functioning it seem he has no knowledge about laws and jurisdiction.' But I have never shown any disrespect towards her."
"Then the Shiladitya episode. We took it as human rights violation and made the recommendation which was again not taken in the right spirit. Similar were the feelings regarding recommendations in the Presidency case."