The Upper Taieri is well-known for its natural values, the report says - particularly a regionally significant scroll plain wetland, trout fishery and endangered native fish.
The report aims to identify the state of the catchment's water quality and ecological health to provide baseline information for future policy changes.
To do this, council staff sampled water from 18 sites, from the Taieri at Sutton to the Upper Kyeburn above Naseby, each fortnight for 12 months as well as testing 10 tributary sites for habitat condition and fish numbers last summer.
Environmental scientist Justin Kitto said in a natural resources committee report, nutrients such as nitrite/nitrate/nitrogen and dissolved reactive phosphorus E. coli bacteria and sedimentation levels were tested.
Excessive amounts of those nutrients or E. coli reduced the health of a waterway and the fish and plants within it.
The testing found nitrogen concentrations were low compared with other parts of Otago, but still exceeded local effects-based guidelines for all flows in the lower tributary and lower main stem sites, he said.
However, phosphorus exceeded the guidelines at the majority of sites for all flow conditions with a "clear increase" between two sites on the Taieri, but did not exceed guidelines in low flows.
"Rivers are most susceptible to prolific macrophyte and algal growth during the summer when river flows tend to be below median flow."
Irrigation run-off was believed to be the cause of increasing concentrations between Linnburn Runs Rd and Patearoa-Maniototo Bridge and at Waipiata.
Discussions with the Maniototo Irrigation Company revealed there were two or three streams which received run-off which flowed directly into the Taieri River, he said.
"Further input from phosphorous is likely from cattle which are present in the Styx wetland and on the banks of the Taieri River in this area."
E. coli concentrations were generally low in low flows, but did exceed the guidelines during all flows with the Lower Lug Creek site having exceptionally high concentrations.
Sediment concentrations were low on the Taieri River. Physical assessments of the smaller streams showed sites where fine sediment would cause concern.
Lower Gimmerburn was of most concern with 65% of the stream bed smothered with fine sediment, Mr Kitto said. The source was likely to be stock access and irrigation run-off.
Good ecological values were shown by trout population and macroinvertebrates were generally found, he said.
"Central Otago roundhead galaxiids were present where trout populations were limited by over allocation of water."
