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The project is the brainchild of the North Otago Sustainable Land Management group (Noslam), which wants to try to reverse the Waiareka Creek catchment's increasing phosphorus levels.
If the sources are identified, the group hoped landowners could take action before new water quality regulations come into effect next year.
With funding from the North Otago Irrigation Company, Noslam has hired University of Otago scientists to carry out water sampling at 70 sites across the catchment, and soil sampling at 19 sites.
University of Otago geography department hydrologist Sarah Mager said the project would evaluate whether organic or inorganic phosphorus deposits in the riverbed and banks were potential sources of the phosphorus in the water.
''The phosphorus cycle is closely related to the sediment cycle,'' she said.
It had a much slower turnover than the nitrogen cycle, and sediment took phosphorus with it.
Because phosphorus has no isotopes, no-one could tell how long ago it was deposited at any site.
''That's why we have to take the sediment approach.''
Soil samples and river sediment samples would be collected once, and water samples twice.
Dr Mager and colleagues have been out on the riverbanks taking water samples and aimed to return to collect soil and sediment samples in the coming weeks.
Noslam member Lyndon Strang said the study was independent, instigated by the group in the interests of sustainable land use.
If the area's natural phosphorus levels were found to be high, Noslam could take the findings to the Otago Regional Council and make a case for adjusting permitted levels under the incoming water quality standards, he said.