Ratepayers will have to dip into their pockets for Hawke's Bay's environment, with rates set to rise by 10 per cent to fund a clean-up of the region's waterways.

Yesterday the Hawke's Bay Regional Council agreed to a rates increase for a million-dollar environmental fund to be included in its 2017-2018 annual plan.

Increasing rates by 9.88 per cent would create the "environmental kick-start fund" which would target "environment hotspots" - including Lake Tutira, Ahuriri Estuary, Whakaki Lake and Wairoa River, Lake Whatuma and the Tukituki catchment, and Karamu Stream.

It would not "fix" issues facing these waterways, but would go toward plans to do so.

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Despite some concern by councillors over the increase, yesterday chairman Rex Graham said taking "a couple of good steps forward" with this fund would send a strong message.

"We know it's limited, we know it's not everything [the community] want but at least it's a step in the right direction.

"Nobody in the public believes we can fix the problem with this amount of resource but at least we're going to begin and get on the road to fixing them."

Other councillors stated the million-dollar figure raised through the increase was a "minimal" amount of ratepayer cash compared with other projects the regional council proposed to progress on.

Some noted there would be "a lot of scrutiny" over what the council achieved with this funding.

The 9.88 per cent rise was one of three options consulted on during the annual plan.

Under the proposed increase, households in the urban Napier/Hastings area could expect to pay $15 and $33 more in the 2017-2018 year - or $3 for Flaxmere.

Households in Wairoa could expect to pay about $15 more, or an extra $16.80 for Central Hawke's Bay.

Concerns were raised by two councillors, Wairoa councillor Fenton Wilson and CHB councillor Debbie Hewitt, who later voted against the 9.88 per cent increase.

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Ms Hewitt said the plan did "a disservice" to the work done by council in the past, and had instead fuelled speculation that council had been "inefficient", and that farmers had not been active in this area.

"There's a huge amount of rural investment to date which has gone unacknowledged in terms of the spend going on," she said.

"In order to be adding another tax on just because we can has disenfranchised quite a number of our rural community."

Although the increase was notified as a "one-off", Mr Wilson noted this was not the case, as the 9.88 per cent was "now the new normal".

The majority of submitters during the consultation process supported the proposed 9.88 per cent rise - with the resounding message that this was the "only option" to ensure action to clean up the region's problem areas.

Many included the provision they supported the increase as long as it was a one-off used for its correct purpose.

Yesterday council also agreed to develop milestones "against which progress in dealing with the hotspots initiatives, funded by the 5 per cent rates increase, will be measured".

The 2017-2018 Annual Plan will be adopted at the end of June, with the rating option coming into effect on July 1.