A council spokeswoman said dredging occurred around the Clive bridge recreation area -but only at the lower part of the river every 12 years due to the expense involved, "costing the ratepayer around $800,000 each time".
"We also clear weed build-up further upstream using the weedboat to keep the channel clear," she said.
This weekend, the spokeswoman said there were other factors making the river shallower which the waka operators were not aware of, such as the low tides, which could have meant there was less water in the river.
Mrs Edwards told Hawke's Bay Today they were not able to choose the times of rides due to the transient nature of their passengers, meaning they could not work to the tides.
Council group asset manager Mike Adye said there was currently also an open river mouth making the river more responsive to tidal changes than if the mouth was closed or narrow.
"Also it means the river is draining more freely, so there is less or no water backed up in the system as happens when the river mouth is narrow or closed," he said.
"Plus it's summer, so there is less rainfall and city stormwater draining into the catchment."
Despite these assurances, Ms Edwards said she worried that if the conditions did not change their venture could be impacted.
During the summer season, every time a ship docks in Napier and is associated with the Edwards' contractor they can look forward to hosting up to three waka-loads of passengers.
If their venture could not continue on the river, Mrs Edwards said they might be impacted financially and would not have the money to maintain the waka.
Otherwise they could have to return to offering rides in Napier, which she felt was not as safe as the river.
"There's more water in Napier but there's also more boats, and people," she said. "That would be good for publicity but the safety of our passengers is paramount.
"We feel comfortable there where we are...we've got people's lives we're responsible for."
Hawke's Bay Tourism general manager Annie Dundas said this was the first she had heard about tourism operators being impacted by this sort of environmental issue.
Without knowing the state of the river, Ms Dundas said she could not comment, however she added: "We want our waterways to be as clean and safe for tourism operators as possible."