Mr Pettigrew said the relaxed approach to water trading was allowing massive amounts of inter-valley trading out of the Goulburn Murray Irrigation District.
“The damage done to the Goulburn River is not from environmental flows, it's from IVTs keeping the banks wet all summer and pumping three times the volume down,” he said.
Mr Pettigrew said the Goulburn was bearing the brunt of massive water demand downstream.
Mr Court said many people had a "complete misunderstanding" of the basin plan.
“And to be quite frank, some legislators have done nothing to correct the misunderstandings,” he said.
“I think the MDBA is doing a good job.”
More controversially, Mr Court said some country towns should go if they can't survive the modernisation of irrigation.
“They’ve suffered since the end of the gold rush,” he said.
“Some of those little communities have to go.”
The senate committee sat in Deniliquin on Wednesday and was moving to South Australia after Shepparton's hearing on Thursday.