The vast majority of high lakes were naturally fishless. There are a handful of exceptions all of which are large, relatively low elevation valley bottom lakes that have native fish.
The rest of the lakes either have an introduced naturally reproducing population, or they are periodically stocked. The largest lakes are stocked by aircraft. Most is done by fixed wing aircraft. The state has a Beaver that has been fitted with a custom made drop tank. Some lakes are stocked with a helicopter. Most of the lakes in the Olympic National Forest are stocked with a chopper these days but almost everything in the Cascades is done with the Beaver. Smaller lakes are stocked by hand. Someone puts the fry on their back and carries them in. The Trail Blazers are the primary volunteers for the WDFW. They stock over 100 lakes per year generally from Lewis County north on the west side and Kittitas County north on the east side. The Backcountry Horsemen pack some fish in in Yakima County and there are various other volunteers and WDFW personnel who are working in Skamania County. There was a Forest Service backcountry ranger who was packing fishing into Gifford Pinchot NF lakes for the WDFW, but he passed away last year.
It used to be that people hoped the fish they put in the lakes would reproduce by themselves. Now we try to do everything we can to avoid having fish reproduce. Most of the time, if they are able to spawn on their own they will overpopulate the lake and wipe out their food supply. This is horrible for the fishing, you get a lake where you can catch a fish every cast, but they are all small and there is no way they can grow larger. Worse, that many fish in the lake can severely impact the native flora and fauna in the lake including amphibians (mainly salamanders) and smaller invertebrates like copepods. The key to avoiding those harmful situations is to plant fish in low numbers. Studies in the North Cascades have shown that fish planted periodically do not compromise the native biota. So when you get to one of these overpopulated lakes don't feel guilty about keeping a bunch of fish.
So, most of the lakes are stocked with low numbers of fish on a periodic basis. That means the lake that is hot one year may not be hot the next year or the year after. One important thing to take away from this is that you should always take your fishing rod to every high lake. The fish are there no matter how remote the lake.
And be sure to fill out a survey form for all your high lake trips. All surveys filled out on the Trail Blazer site are strictly confidential and are distributed to the appropriate WDFW biologist at the end of the season.
High Lake Angling Survey That was probably a lot more then you wanted to know...
Brian