Los Angeles county district attorney Nathan Hochman said some of the alleged incidents had happened too long ago, while there was not sufficient evidence to charge the 56-year-old, whose legal name is Brian Warner, over some of the other claims.
The identities of the women who spoke to authorities were not revealed, but Game Of Thrones actress Esme Bianco, who sued Manson in a case that has since been settled, said she was part of the criminal investigation.
Mr Hochman said: "We have determined that allegations of domestic violence fall outside of the statute of limitations, and we cannot prove charges of sexual assault beyond a reasonable doubt.
Marilyn Manson will not be charged following a lengthy investigation into sexual assault and domestic violence allegations, prosecutors have said.
LA county sheriff's detectives announced in early 2021 that they were investigating Manson for incidents between 2009 and 2011 in West Hollywood, where he lived at the time.