Senator Waters said strong action on climate change and social justice policies will sit side by side as priorities in the next term of the federal parliament.
The Queensland senator, who won the top job uncontested at a party room meeting on Thursday, said the Greens could "walk and chew gum at the same time", maintaining their focus on social and environmental challenges.
"We certainly don't resile from our strong stance on social justice issues," she told ABC Radio on Friday.
"We will always call out atrocities, and we will always work to make sure that people's daily needs are met and that we're looking after the planet."
Senator Waters was elected to the position following the shock defeat of former leader Adam Bandt in his lower house seat of Melbourne.
Mr Bandt was one of three lower house MPs from the Greens to lose their seat at the election, along with Stephen Bates and Max Chandler-Mather, after the party suffered a swing away from them in the inner cities.
The party faced attacks from Labor, who criticised it of obstructing social housing legislation in the Senate, and the coalition, who accused the Greens of being a "Jew-hating, anti-Semitic party" for their criticism of Israel.
The Greens' commitments to nature has buoyed environmental groups after they were accused of straying from their roots and getting distracted by other progressive causes.
"We think this is a welcome sign that the Greens are getting back to core business, which is protection of climate and the environment," Australian Conservation Foundation climate and energy program manager Gavan McFadzean told AAP.
"In terms of their campaigns and their public work ... it would be good for them to have a stronger focus on climate and environment this term."
Just because the Greens had been outspoken about the actions of the Israeli regime did not mean the party were anti-Semitic, Senator Waters said.
"There is no anti-Semitism that is acceptable anywhere. Likewise, there's no Islamophobia that's acceptable anywhere," she said.
"We want peace in that region, and we want kids and women and everyone in that region to have self-determination."
Acting Prime Minister Richard Marles said while Labor often disagreed with the Greens, he congratulated Senator Waters on her appointment as leader.
"It is right to acknowledge and congratulate Larissa Waters on becoming the leader of the Greens. It's obviously a significant achievement for any person to lead their political party," he told reporters in Adelaide.
"We will see what her leadership brings as it unfolds for the Greens."
However, the Greens hold the balance of power in the Senate after retaining 11 seats, with Labor only needing support of the minor party to pass laws in the upper house.
The Greens retained one lower house seat - Ryan, held by Elizabeth Watson-Brown.
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