I found this report on the Parliament of Victoria's website. It's called Inquiry into flood mitigation infrastructure in Victoria 2011. One witness stated:
The reorganisation of the Torrumbarry system was completed in 1969-70 with the dredging of the Pyramid Creek from Kow Swamp to the Kerang Lakes. This enabled flows released from Kow Swamp to reach the Kerang Weir pool in 36 hours instead of 3½ days. Throughout the 1990s all streams, creeks and low-lying areas that carried occasional water were cleaned by dredging.Were there any protests at the time? Did everyone agree with the process? Didn't anyone think about the creatures and plants that lived in the waterways? And the floods weren't mitigated so was it all for nothing?
Maybe there has been a rethink. In the August 2014 edition of the DEPI newsletter Fish-e-fax I found this:
Thanks to $60 000 of funding from recreational fishing revenue, fish habitat in Pyramid Creek is set to be improved. Snag piles will be placed into the creek by the North Central CMA to provide native fish with shelter from fast currents, refuge from predators and sites for feeding and spawning. The project will help the waterway become a key pathway during fish migration and will boost the permanent population of native fish.