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At least one of the billboards will be placed near the Selwyn River where potentially toxic blue-green algae has been found.
A Greenpeace spokesperson said the three billboards aim to "remind the prime minister of her promises on New Zealand rivers".
The first billboard will show a "larger than life image of Jacinda Ardern", with a quote from her reading "we will clean up our rivers".
Greenpeace says it is worried the Government "might have overlooked" cutting synthetic nitrogen fertiliser to protect rivers as part of its freshwater reforms.
The billboards will be erected by Greenpeace activists upstream from Coes Ford on Thursday.