While the Waitaki and other rivers are dropping towards normal levels, all are still badly discoloured.
The same applies to the popular Waitaki lakes, making fishing extremely difficult.
After heavy rain and spilling by Meridian Energy Ltd just after Christmas, the Waitaki River reached 1738cumecs.
Other popular fishing rivers, such as the Ahuriri, which reached 353cumecs, were also in flood.
Yesterday, the Waitaki River was down to about 450cumecs, but still discoloured by glacial silt.
Water was still being spilled at 60cumecs down the Tekapo River and the Ahuriri, while back to normal flows, was rising again yesterday.
Central South Island Fish and Game Council officer Graeme Hughes predicted it would "be several weeks" before the Waitaki River was clear enough for successful fishing.
The high flows had stripped out didymo, which would please salmon anglers.
The major salmon runs into the river usually occur next month and in March and Mr Hughes hoped that, without more significant rain, the river could be suitable by then.
Visibility in the Waitaki River on Tuesday was only about 100mm.
The limit for salmon angling was usually regarded as being able to see your toes when standing in knee-deep water, he said.
It was being affected by fine glacial silt and some discolouration from sediment remaining from the earlier high flows.
Mr Hughes flew over the catchment on Monday and said other rivers were still dirty.
He was surprised the Ahuriri was still discoloured, even although flows had returned close to normal over the past 10 days.
The discoloured water and spills from the glacial storage lakes was also keeping Lakes Benmore, Aviemore and Waitaki discoloured, disrupting fishing by the thousands of January holiday makers.
