Paul
Like Jim says it is down to lack of food in the river system. The Dee is a very oligotrophic river (Lacking in plant nutrients such as phosphates, nitrates, and organic matter, and consequently having few plants and a large amount of dissolved oxygen throughout) because it runs off hill ground with a lot of acid granite rock and poor infertile soils. Because of the lack of food, once the young fish grow above parr size, almost all of them have to go to sea to feed.
The headwaters of the Don runs off gabbro and mica-schist rocks which produce more fertile soils, hence more nutrients in the river, hence more food for the fish. There is an old rhyme which is based on the difference in the fertility of the two valleys which goes
"Aye mile o' Don's worth twa o'Dee
Except it be for fish and tree"
So I guess the Dee was always a better salmon river. Maybe because there are so few brown trout to feed on the young salmon parr.
Irvine