A weed-cutting boat had gone out on the river above Havelock North about three weeks ago. The weed had been caught near Essex Park, which was where weed had been planted a couple of years ago and since undergone "exceptional growth".
This boat is part of the work undertaken by community project Operation Patiki and the council to clean the river.
This problem has occurred in the past, caused as the boat only works in segments, so the cut weeds travel downstream and clog the waterway.
The spokeswoman said the circumstances this year - from the weed growth to very little rainfall last month - led to the more extreme result. The construction of the nearby Whakatu interchange had also played a role, as it changed where the weed was caught, which used to be further upstream.
"It's going to continue so staff are looking at changing the weed cutting or developing a weed catcher," she said. "We have to control the weeds."
Due to the high number of fish getting caught, council scientists yesterday also examined the river flow, water quality, and oxygen levels.
It was determined water quality was not a factor and that, although oxygen levels were lower than normal, these were not enough to explain the incident.
The council had tried to remove weeds in the past, but they just grew back.
It was hoped the weed boat would get back to work on the river early this week.
At the weekend marae member Tom McGuire, who helped set up Operation Patiki in 2008 to clean the river, told Hawke's Bay Today the fish died because they swam up the river, flipped on top of the thick weeds and got stuck.