Scientist Kathryn McArthur made the comments during a hearing at Ascot Park Hotel in Invercargill.
She was representing the Royal Forest and Bird Protection Society of New Zealand to provide evidence on freshwater management, water quality and ecosystem health for the Southland Water and Land Plan.
The proposed document aims to address declining water quality and manage land-use activities that contribute a significant level of contaminants.
In her evidence, she assessed the Land Air Water Aotearoa data from 56 sites in Southland rivers across five freshwater management units to determine the general state of water quality and the potential for adverse effects on ecosystem health and associated values.
She said faecal contaminants, indicated by E.coli, were elevated in many rivers in Southland, compared with nationally.
At nine sites - Otautau Stream, Opouriki Stream, Bog Burn, Winton Stream, Tussock Creek, Otepuni Stream, Waikawa Stream, Oteramika Stream and the Mataura River - the concentration was high enough to be of significant concern for recreational safety.
Under cross-examination by Environment Southland counsel Philip Maw, she said the level of nitrate-nitrogen was another important factor to manage.
She would not know the exact levels in Southland rivers, as they depended on a number of factors.
"What we do know is that 1mg per litre is a quite high level of nitrate-nitrogen in the terms of a likely effect in ecosystem health."
She said because a large number of water bodies were already significantly degraded and at high risk of further degradation, some critical changes to land use and land management practices should be introduced urgently.
"In order to deal with the current water quality problems, a region-wide response is needed."
The hearing, in which multiple agencies have appealed the proposed plan, continues until next week.
