An MoE official said the sites were generally chosen for their susceptibility to risk factors.
"It focuses on the suitability for swimming at popular swimming spots, and does not give a comprehensive picture of the overall state of New Zealand's waterways."
Massey University ecology lecturer Mike Joy said the results showed that a clear difference between good and bad sites related to whether they were upland or lowland. All the downstream sites failed because of run-off from dairying and effluent from wastewater plants.
But NRC senior monitoring manager Colin Dall said it was not that clear-cut.
"Although farm run-off may well contribute to poorer water quality in lowland rivers, it is not the only cause."