Ahead of a statement to parliament on Thursday on the AUKUS security pact, Mr Marles said there was a renewed focus on sovereignty ahead of the country's acquisition of nuclear submarines.
A formal announcement on how Australia's nuclear submarine operations would look is expected in coming weeks.
Mr Marles told ABC Radio despite the UK and US being part of the security pact, the submarines would be under Australian control.
"What you will really see is a collaboration between America and the United Kingdom in helping provide Australia with this capability ... it is genuinely a three-way solution," he said.
"Once an Australian flag is placed on these submarines in the future, they will be completely under Australian control and they will act in Australia's national interest."
In the speech, Mr Marles will say nuclear-powered submarines will help build on joint initiatives Canberra already runs with Washington, including through the Five Eyes security partnership.
"The threat of armed conflict is less remote and foreign interference is more prevalent than ever," he will say.
"It has never been more important to guard, reinforce and enhance our sovereignty."
Mr Marles tried to allay concerns Australia could be undermining its sovereignty by having significant technology sourced by other nations.
"It is a massive step change in our capability. It is not unique that we are acquiring technology and capabilities from countries abroad that we wouldn't be able to develop on our own," he told ABC Radio.
"The joint strike fighter is an example of a collaboration across a number of nations that we wouldn't have been able to do on our own but we have complete sovereignty over the joint strike fighter."
Mr Marles says joint facilities with the US in Australia such as Pine Gap, the geological and geophysical research station and the solar observatory enhance the nation's security.
"These facilities also contribute to global counterterrorism efforts, verification and compliance monitoring of international arms control and disarmament agreements, as well as early warning of ballistic missile launches," he will say.
"Full knowledge and concurrence does not necessarily mean Australia approves each individual activity or task undertaken.
"It evolves in line with advancements in technology and with emerging opportunities, threats, risks and trends that affect Australian and US capabilities."
UK Defence Secretary Ben Wallace has said the submarines would be a joint endeavour between the three nations.
"Whether that is the sharing of technology and the understanding of how to do it, the sharing of the build or the sharing of the design," he said while hosting Mr Marles in London last week.
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