Under the new agreement, both councils are able to contract for the removal of rubbish in "hot spots" where it is found both in the water and on land.
Ohinemutu, Utuhina Stream and its tributaries have been identified as the first areas to focus on.
The spokeswoman said it was working with local landowners and operators about mitigating the rubbish issues in those areas.
"Council also works with a number local volunteer groups for rubbish collection and if a member of the public wants to organise a rubbish collection day, the council will support them by providing rubbish bags and taking rubbish away after the clean-up has taken place.
"Illegal dumping of rubbish has financial, social and environmental costs for the community. While we do our best to clean up the rubbish as soon as we are aware of it, it shouldn't be there in the first place."
Rotorua Lakes Council infrastructure general manager Stavros Michael said the Linton Park Reserve, which the Utuhina Stream flows through, was also a hot spot for illegal dumping and the council's waste contractor Smart Environmental had carried out 17 clean ups since February this year.
"Green waste such as lawn and tree clippings seems to make up a large portion which is disheartening when it costs nothing for people to compost in their own backyards.
"Illegal dumping is a community problem and people have to take personal responsibility for doing the right thing in disposing of the waste they generate."
Local woman, Christina Kaiser said she had been battling both councils since August to have rubbish removed from the waterway, where she regularly walked.
She said lining the stream edge were cans, plastic bags, household items, a pile of sheep tails and more.
"I am just getting really frustrated and sick of looking at all the rubbish.
"I have been jumping up and down and not one item has been touched."
She said the rubbish runs from the top of the reserve to the bottom and it was all just going to end up in the lake.
"I walk through the Redwoods and I don't see any rubbish, but this reserve has just been left and it doesn't look good," Kaiser said.
"I don't know what needs to happen to stop people dumping but more needs to be done to clean it up."
Kaiser began emailing the councils in early August and said she was glad to see "the ball has finally started rolling" when last week she received a call from Smart Environmental and took their area manager Scott Brown out to show him where the rubbish was located.
Brown said since her first request in August, Smart Environmental teams had visited the area four times and cleaned up about two tonnes of dumped waste.
"Rubbish is often dumped out of sight and in places that are difficult to access, meaning cleanups don't always happen straight away.
"There are locations such as stream edges and hillsides that require special equipment or the right weather to be able to remove the rubbish."
He said the reserve is quite boggy so it is very difficult to access some of the rubbish without damaging the reserve or getting stuck.
"We are disappointed about the amount of rubbish that is dumped around the district and we will be cleaning this particular area up as soon as we can."
Malfroy Primary School principal Nicky Brell said the school would be interested in partnering with the councils to help with the cleanup.
"Our kids want to keep that work going and to keep the reserve free from rubbish.
"There are a lot of positive opportunities for them in taking part in these cleanups and to provide education about the environment and the impact of rubbish dumping."
