They were on their way to the Himalayan Sikh shrine of Hemkund Sahib.
After initial investigation the police suspect that the woman's husband allegedly slit the throats of both his wife and daughter and fled after locking them in their room at the hotel, SP Chamoli Tripti Bhat said.
A search has been launched to nab the woman's husband who is missing, she said.
The family from Ambala in Haryana had arrived at Govindghat on their way to Hemkund Sahib on Monday evening and checked into the Ganga hotel here to spend the night before continuing their trek.
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A few hours later, the hotel staff suspected that something was amiss and called the police.
When the door of the room was broken, the mother-daughter duo was found lying in a pool of blood, their throats slit, the SP said.
An intense search is on for the husband of the woman, who seems to have committed the crime, she said.