Only three of Nova Scotia's waterways will remain under federal protection under new legislation brought in by Bill C-45, CBC News has learned.

The omnibus bill changes the Navigable Waters Act and removes 99 per cent of the country's lakes and rivers off the protected list.

The only waterways still protected in this province are the Great Bras d'Or lake, the Bras d'Or Lake and the LaHave River.

Critics said without federal oversight, the rest of the rivers and lakes could be developed without any public notice or ministerial approval. For example, proposals for big pipelines and interprovincial power line projects will no longer have to prove they won't damage or destroy navigable waterways in Canada.

The federal government said the changes will reduce red tape that was holding up projects along waterways.

They also said many waterways will still be protected under other laws.

Aboriginal groups across Canada have been voicing their concerns with some of the changes to legislation included in the bill which might have an impact on treaty rights concerning native lands and waterways.

Residents of the Millbrook First Nation community, along with others, have embarked on a four-day fast to show solidarity with Chief Theresa Spence and her 17-day hunger strike in Ottawa.