Two popular freshwater sites where tourists and locals swim were red-flagged for failing to meet recreational water quality guidelines several times this summer.

The Kerikeri River near the Stone Store failed to meet the clean water standards on four out of 14 tests and the Hatea River at Whangarei Falls failed three of the 14 samples.

Samples were taken from 47 popular coastal sites and 13 freshwater Northland locations each week between November 23 and February 22.

Northland Regional Council's regulatory services manager, Colin Dall, said it was generally expected some freshwater sites returned elevated faecal indicator bacteria levels after heavy rainfall.

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Freshwater sites are more likely to be affected by water run-off from land, a situation expected to improve due to increased level of resource consent compliance by farmers.

"The council expects to see improvements in water quality at freshwater swimming sites as a result of the various work being undertaken by farmers and other landowners, such as fencing of rivers, the farm water quality plans it prepares for farmers and the ongoing compliance monitoring of wastewater discharges it undertakes throughout Northland," Mr Dall said.

Action over amber or red flags can include investigations to establish the source of contamination and public warnings not to swim or gather shellfish.