The regional and district councils say it is due to a storm and high winds and the smell will remain while some of the weed dries up or is washed away.
Lime Cafe manager KV Ranwat said the smell was affecting customers, especially when sitting outside his café on Whakaue St.
"Sometimes we get a whiff even inside the restaurant."
He said it wasn't so bad on Monday morning because the wind was redirecting the smell but when the wind changed direction and it was muggy outside it was worse.
"If [the councils] can sort it out pretty quick that would be good."
He said it was yet another challenge to the business on top of Covid-19.
Brew Bar owner Paul Croucher said the smell had been particularly bad on Friday.
Raewynne Williamson, who lives on Whakaue St, said she could smell the stench from her home and her workplace on Pukaki St.
She said lake weed had always been an issue but she'd never known it to be this bad for so long and it was a bigger shame now since the area had had so much money spent on it to make it look so good.
"You almost need a clothes peg on your nose when you're walking down there."
She said they had glass fencing across their decks which helped keep the smell away but as soon as you went on the footpath outside, the smell hit you.
"I see people out there eating and think to myself it must be horrible for them.
"They're working hard to try and get rid of it but it's just terrible. It smells like rotten eggs."
On Monday, a woman who wanted to be known only as Lisa, said it was "a shame because it looks beautiful but it smells terrible".
Her friend, Lauren, said it smelled like raw sewage and needed to be cleaned up.
Both were seen covering their noses as they approached the lagoon at the lakefront, which was bordered by a concrete shoreline and the boardwalk and where much of the stench was concentrated.
Bay of Plenty Regional Council lakes operations manager Andy Bruere said a storm a couple of weeks ago washed weed from weed beds in the lake to the shore.
"It is a natural event that can happen if we get strong wind conditions that break the weed away from its bed in the lake."
He said the cleanup cost had come to about $20,000 so far to run a weed harvester.
"The smell will abate as the weed is removed. It is likely that some areas where we cannot collect the weed will remain and cause some odour until they are washed away, but the current operation removes the bulk of the weed."
He said the mass of weed smothers any natural organisms.
"As it breaks down it removes all the oxygen from the area and of course this is fatal to aquatic life. Removal as soon as possible is the best option."
Bruere said the regional council and Land Information NZ worked to address weed issues on the lakes.
"It is possible to undertake more weed control at the source where the weed is generated, but this needs to be balanced against the cost of doing this and the likelihood of it being brought ashore in a storm.
"Mitigation is a mix of in-lake control and weed removal if a big event occurs. Council is involved in both actions and moves quickly when there is an event such as this to get it removed as soon as possible."
He said the regional council received three service requests relating to lake weed this year, all received between February 14 and 18.
Rotorua Lakes Council sport, recreation and environment manager Rob Pitkethley said the weed on the lakefront was a result of Cyclone Dovi.
"Rotorua experienced 80-plus km/h northerly winds. This resulted in large amounts of weed breaking off and washing up along the lake edge."
Asked if the lakefront boardwalk or associated redevelopment had posed any challenges to the weed clean up, he said it had not been a problem.
"In the past, the weed would have washed up in the same way, with some coming ashore, but the majority being left in the shallow edges of the lake."
However, he said where access for the weed harvester was an issue, such as shallow areas, the weed would remain until it blew back into the lake, where it would naturally break down.
"It's likely that the odour will abate as it either moves away from shore or completely dries out.
Rotorua Lakes Council has collected 29 truckloads or 260m3 approximately of weed from the lake, it said in a statement.
"The weed has been taken to an old composting yard where it will dry out and decompose. Due to the levels of heavy metals in the weed, it's not suitable for home composting."
The council also said the current cost to remove the weed was "approximately $15,000" but costs may increase with ongoing work as required.