Strong action on climate change and social justice policies will be priorities for the minor party as it enters a new phase following the shock defeat of Adam Bandt at the federal election.
The former party leader was evicted from his lower house seat of Melbourne, alongside fellow MPs Stephen Bates and Max Chandler-Mather, after the Greens 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.
Senator Waters, a former environmental lawyer, said she wanted the Greens to have a role in rewriting environmental protection laws, which the government has promised to do this term.
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."
But Senator Waters, 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."
Anti-Semitism envoy Jillian Segal earlier in the week said some of Mr Bandt's comments about the Jewish community were anti-Semitic and the Greens' weakened result in the election showed the Australian public voted against extremism.
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."
Despite losing three out of their four lower house seats, a swing to Labor in the Senate means the Greens now hold the balance of power in the upper house.
As a result, the government can decide to work with them exclusively to pass legislation.
But the Greens still run the risk of being dealt out of contentious issues such as environmental protections if the government decides it has a better prospect of getting the laws passed with the support of the coalition.
"We are very keen to be able to rewrite those laws and actually protect nature and take action on the climate crisis that's wreaking so much havoc on this beautiful planet and on our lives," Senator Waters said.
"The choice is there, really, for the government: do they want to do a proper job, or do they want to stick with with John Howard's laws from last century?"
The Greens retained one lower house seat - Ryan, held by Elizabeth Watson-Brown - and 11 seats in the Senate, where they will hold the balance of power.
