Tomorrow sees the start of the salmon fishing season on the River Tay but there are troubled waters swirling around the king of fish

Every 15 January (barring days "snappit up by the Sabbath"!) for more than 60 years, a great company of anglers and their friends have gathered at Kenmore to celebrate Scotland's king of fish. For a good few years now, the anglers have marched to the bankside behind the splendid Vale of Atholl Junior Pipe Band, there to see the river christened with a dram of the "aul' kirk", the first coble launched and the first casts made.

What does it matter if ice clogs the rod rings and only a low and hesitant sun illuminates the scene? The fly is in the water and could at any moment be seized by one of the large and active fish that lead their charmed lives in the imaginations of all true "brothers of the angle".

What a fuss about rather a primitive fish; however, the plain fact is that wild salmon matter. Alone among the economically important fishery resources of the North Atlantic, it is just about the only one which is not heavily exploited by fishing. Not only that, but such fishing as does take place in the rivers, estuaries and coastal waters of these islands is entirely under national control.

A lightly fished resource of high unit and total values and controlled by the local interests who have most to gain from it – surely there is no better formula for sustainable management? Add to that happy circumstance the fact that, thanks to the decline of heavy industry, the total area of fresh water able to support salmon production is actually increasing, and one is bound to pose the rhetorical question, "Why on earth are there not more of them?"

But wild salmon resources are currently so depleted that some populations no longer sustain an exploitable surplus, or even provide enough adult spawners for their offspring to make full use of the juvenile habitat available to them in the rivers. It is time to look hard at what has gone wrong.

Although there are still unresolved pollution and obstructional problems in rivers and estuaries, a large body of evidence from carefully monitored rivers in Ireland, Scotland and Norway shows that an increase in mortality rates between the young salmon (called "smolts" at this stage) entering the sea and the adults returning after one or more winters at sea lies behind the current shortage of salmon of all sea ages.

Back in the late 1960s and early 1970s, as many as a third or more of the smolts would survive to re-enter our coastal waters as adults. Nowadays, we are lucky to get back a tenth. Not surprisingly, for they are exposed to the increased rate of attrition longest. There has also been a marked reduction in the proportion of older, sea-age salmon in the returning populations; that is to say, fish that have survived at sea for two or more years before coming back.These older fish have a value out of proportion to their numbers, because they tend to run the river earlier than their younger fellows and thereby contribute to the fishery for longer than younger, later-running fish. Indeed, for beats like Kenmore, at the head of long rivers such as the Tay, they are the principal resource for a good part of the season.

Interestingly, tagging experiments have shown that these earliest-running salmon tend to be more responsive to the angler's fly than later ones. This greater responsiveness is probably because they have entered the river as much as a year or more before spawning and are therefore less subject to the suppression of feeding reflexes caused by the presence of sex hormones in their bloodstream.

Final confirmation that a sustained increase in the marine mortality rate is the principal reason for the relative rarity of older, sea-age salmon comes from observing the near disappearance of fish which have survived to spawn more than once.

The current challenge for salmon science is to define the underlying causes of the high loss rate at sea and to see what potential there may be for remedial action. The scope for further reductions in catch rates is very limited. High-seas fishing for wild salmon at West Greenland, Faroe and the Norwegian Sea is now largely a thing of the past, and coastal interception fishing has also been much reduced. The economic effects of the ready availability of farmed salmon have played a part in the reduction of both types of fishery, but the cage culture of salmon has also created problems for wild fish. The principal problems, such as the fatal infestation of wild salmon and sea trout with sea lice and the contamination of wild spawning populations with escaped farmed fish, appear to be relatively local.

The jury is out, however, on the wider effects on the health of wild fish of encounters with potentially infective escaped farmed salmon in places such as the Norwegian Sea.

Another known cause of loss is the inadvertent capture of juvenile salmon by vessels, principally from eastern Europe, fishing at the surface for mackerel and herring in the Norwegian Sea. The extent of the losses has yet to be defined, but it could be greatly reduced by dropping the trawl headline five metres below the surface.

Less tractable is the problem of seal predation, especially by the Atlantic grey seal. It is possible that one reason this problem has arisen is the widespread practice – in fisheries managed by quota – of dumping large quantities of dead and dying fish at sea. This provides meals for seals at minimal energy cost. Prohibiting this abhorrent practice might well prove beneficial to salmon, if not to grey seals.

The most fundamental problem of all is to define the place of the salmon in the changing ecosystem of the North Atlantic. To do that, we will need, as a minimum, to know the migratory pathways and diurnal movements of the fish, the water masses occupied by representative populations at different stages of their marine lives, and the status of the prey and predator species (including vessels fishing for industrial and human consumption) with which they interact.

A surprising amount of progress has been made and there is a general consensus that climatically driven changes in plankton production in the southern part of the marine range of European salmon populations are a major part of the problem. Unfortunately, this is one problem over which we have little short-term influence. In the meantime. we must do all we can to look after the salmon while we have them in our care in the river.

• To Sea and Back: The Heroic Life of the Atlantic Salmon, by Richard Shelton, is published by Atlantic Books, 18.99.

• The official opening of the River Tay salmon season will be held at 9:30 am tomorrow, at the Kenmore Hotel, Kenmore, Perthshire (01887 830205).

• Mark Stephen, of BBC Radio Scotland's Out of Doors programme, will conduct the opening ceremony, along with writer Ally Gowans. Jane Grimley, of Dewar's World of Whisky, is offering the toast ahead of the first lines being cast.

• This is a public event, and those attending will be treated to free coffee, bacon rolls and a wee dram. The event has been taking place at Kenmore since 1947, and last year raised more than 70,000, via sales of fishing permits, for the charities Angling for Youth Development (AFYD) and the Children's Hospice Association of Scotland (CHAS).

Richard Shelton will be on hand to sign copies of his book. There will be free casting tuition on offer all day from AFYD instructors, while fishing permits for opening day cost 25.

• The Kenmore Hotel beat extends approximately two miles on both sides of the Tay. The angler who lands the biggest fish anywhere on the Tay system on opening day will walk home with the MacTaggart Kenmore Trophy and a gallon of Dewar's Whisky.

• For more information, visit flyfish-scotland.com.