Starting with the spring of 2008, all Chinook stocked into the Lake Ontario watershed have their adipose fin clipped. Theoretically all stocked fish in Lake Ontario should have had their adipose fin clipped; while natural salmon would have an intact adipose fin.
The fish stocked in the spring of 2008 were from eggs collected in 2007. The normal life cycle for Chinooks is four years so any salmon stocked prior to 2008 should have already spawned.
One thing we at MEA learned last year was that most of the males spawned after three years. And I am not referring to Jacks. Last year when we collected eggs from the credit, the males were clipped (ie stocked in 2008 or later) while the females were unclipped (stocked prior to 2008). It is possible that some fish will spawn on a 5 year cycle. We didn't know about the 3 year cycle for males until last year... so who knows what else we don't know. I wasn't involved in the egg collection this year but I understand that the vast majority of fish in the credit were clipped. So there doesn't appear to be significant number of 5 year old fish in the credit.
In summary, you should be able to determine if the fish are stocked or not by checking to see if they have an adipose fin. The adipose fin the small fin located just in front of the tail on the top of the fish.
Many of the the Chinook salmon are stocked directly into Lake Ontario and there has been a significant increase in pen reared salmon in recent years. These fish would not have a 'home' river to return to, and may seek other rivers to spawn. Stocking sites, and the number of fish stocked in each site has remained mostly constant over the years. However, in some cases extra fish are stocked at the mouth of the Niagara to make up for short falls on the U.S. side.
The main change in stocking has been an increase in pen projects. The pens are located near the previous sites but pen reared fish are believed to have better survival rates and a stronger urge to return to the same area. These factors could account for an increase in particular rivers.
Weather can also account for changes. Rainfall and water temperatures will impact the timing and size of runs in the fall. Favourable conditions can impact the survival rate of fish in the spring. I suspect that natural salmon would be subject to greater variations in numbers from year to year.
I hope this helps.