Ganguly, who was on the run, was arrested on Friday by a joint team of policemen from Goa and Delhi, and was flown back to the coastal state on a transit remand in the early hours of Sunday.
"The accused will be produced before a local magistrate today (Sunday), where we will be seeking police custody," a senior police official said.
The accused swimming coach has been booked at the Mapusa police station in North Goa district, under sections 461, 354, 376 and 506 (ii) of the Indian Penal Code, Section 8 of the Goa Children's Act and Sections 6 and 8 of POCSO Act.
The victim has accused Ganguly, who had served as the chief coach of the Swimming Association of Goa for nearly two and a half years, of molesting her.
The complaint followed hours after a video of the coach, who has since been banned by the Swimming Federation of India, allegedly molesting the minor girl went viral on social media on Thursday, sparking uproar across the country.
A complaint was filed by the victim's father with the Kolkata Police, but the case was subsequently transferred to the Goa Police, after the victim revealed that the controversial video was shot in the coastal state.
( With inputs from IANS )