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The study, jointly funded by the Institute of Environmental Science and Research (ESR) and Environment Southland, tested water samples across the region and targeted rivers that were known to have high concentrations of E. coli.
Eight shellfish-gathering sites were also monitored for levels of faecal indicator bacteria (faecal coliforms, E. coli and enterococci) between August 2016 and August 2017 and results suggested only one site, Riverton Rocks at Mitchells Bay, should be considered safe for the collection of shellfish intended for human consumption.
The study, released last month, also showed about 50% of river samples had ruminant pollution present from cows, sheep, deer and goats, which increased after rainfall.
Faecal pollution from ruminants typically contains bacteria such as campylobacter, cryptosporidium and salmonella, which are a concern for human health.
The dominant faecal pollution in 80% of the rivers sampled was from wildfowl such as geese, swans, gulls and ducks.
Environment Southland science manager and report author Dr Elaine Moriarty said while the amount of faecal pollution from wildfowl was high, the risk to human health from that source was low but the risk of swimming in a river with even a small amount of pollution from human or ruminant sources was very high as the diseases this pollution carried were more readily transmitted to humans.
She said the results were not necessarily unexpected, as sites known to have elevated levels of E. coli were chosen to be tested.
''There are easily accessible and known to contain previously high numbers of bacteria ... there are probably hundreds of sites that shellfish can be gathered,'' Dr Moriarty noted.
The purpose of the study was to identify the sources of pollution so better preventive measures could be implemented.
Five reports were made, one for each main river catchments, Oreti, Aparima, Mataura and Waiau.
The Oreti report said, ''Waterways in the Oreti FMU are vulnerable to high levels of faecal contamination ... campylobacter was isolated from 88% of samples. Wildfowl, ruminants, poultry and humans were all identified as being sources of campylobacter'', which is similar throughout catchment samples.