Only a federal royal commission with "real teeth" can uncover the corruption and mismanagement that is killing the nation's biggest river system, the Murray-Darling Basin, leading Indigenous groups say.

The demand was a centrepiece of issues raised by hundreds of water activists who gathered in Canberra on Wednesday, including some who staged a protest in the Marble Foyer of Parliament House.

Protest against fracking and Indigenous issues in the foyer at Parliament House on Wednesday. Credit:Dominic Lorrimer

"The federal royal commission must have real teeth," Michael Anderson, acting chair of the Northern Basin Aboriginal Nations, said. "It's got to have the power to recommend prosecutions."

The call, which dovetailed with the Greens' plan to introduce a bill for a royal commission in the Senate, is aimed at breaking up "an incestuous relationship between the National Party and farmers" that had led to the unsustainable over-allocation of water extraction from the rivers, Mr Anderson said.