Higher elevation = less growing time for fish, but also less fishing pressure. That means plentiful but tiny trout for most of the JMT. Even so, flame roast the little ones and there's no need to de-bone.
Little Yosemite Vly - 10" browns. Low light helps in placid waters
Upper Sunrise = the only cutthroat on JMT
Cathedral Lake overfished, the stream down toward Tuolumne has some 9" brookies
Tuolumne Meadow- cautious approach + small terrestials (esp black ants or #10-12 tan/yellow hopper) near the bank
Skip rafferty+ireland to concentrate on Lyell fork (9mi). This is the last great fishing til Minaret Creek (well after Donahue Pass)
1000island lake = tons of pressure. Outlet stream best bet, nymph fast water or dry caddis the pockets Long walk to inlet stream good idea. Grasshoppers. Like Garnett, Shadow, and Rosalie Lakes, just fair.
Ruby Lake, teeming with large trout, better than Emerald (both rely on stocking) Some true giants hiding here.
Garnet-Shadow-Rosalie-Vivian all rely on planted fish, sparse, stunted. I had good luch at Rosalie from atop an east shore boulder.
Gladys - I took my biggest lake trout here, fought like mad breeching repeatedly a couple feet out of the water. Last chance to fish before the long dusty descent to Devil's Postpile.
Minaret Creek (great for an hour or so) -Loaded with colorful 9" brookies
Middlefork San Joaquin @devils postpile -12" browns Tan Elk Caddis #12-#16
Nothing til Crater Creek @Crater Meadow (not upper meadow) Big trout in tough to reach brushy runs
Thomas Edison reservoir - Too windy when I was there, didn't try.
Deer Creek, super fishing! - Ignore north branch, go to main south branch. Many mosquitoes.
Duck Lake detour (no camping) for plentiful trout
Purple Lake, overrun but planted plentifully 9-11", use #16 Elk Caddis. Outlet creek also good wherever u can find holding water. Inlet was occupied by a camper ten feet from shore with his dog which confined me to the north shore and very poor results. Skip and hurry to Fish Creek.
Lake Virgina, state record golden trout caught here. #22 tiny yellow stones #14 black caddis flies #16 gray-brown crickets. Stick to the north side, I got skunked on the east shore.
Fish Creek - as fun as the upper meadow is to fish, only fingerlings dwell here. Far better fishing is to be found in the deep dumps and wide pools a little ways below. River access becomes more difficult (therefore protected!) the nearer you get to Cascade Valley JCT
Bear Creek at Lake Italy trail JCT - Super fun fishing, lively if smallish golden attacking hard. Even when they grow to 9"+ they remain skinny.
Marie Lake - Spent an entire day here. Great fun if you walk out onto the peninsular shore. Wherever you spot a fish patrolling the shore, they'll rise to your fly 100% of the time. Decent size too.
Sallie Keyes Lake - Sadly had to make time and pass up these very promising waters. Wish I'd planned better to spend at least half a day exploring here.
Muir Trail Ranch - The San Joaquin River is world famous and ice cold. This was one place where my sealskin socks and sandals were inadequate. The river is very wide and quite swift even in late August. The biggest risk is that you'll abandon the JMT to fish down this amazing river while warming yourself each evening in Blaney Hot Springs! I'll be back here with time, fact.
Evolution to McClure Meadow - I made the mistake of waiting to reach McClure before trying to fish. It was far too shallow there. I may have passed up some excellent opportunities closure to Evolution Meadow.
Evolution and Sapphire Lake - Fun fishing here, the inlet at Sapphire was full of feisty fingerlings. The shore is so soft though, you'll find yourself sinking past your ankles. Moving over to granite shores takes you away from the trout.
Le Conte Canyon to Grouse Meadows - Gorgeous waters and full of hungry, but alas tiny, trout. Nymphing in deeper waters produced quite a few keepers.
Golden Staircase to Palisades Lakes - The higher you climb, the more gorgeous the vegetation and rock pinnacles. Near the end, desolate scree slopes have morphed into lush green shores and orange streams sparkling with trout belly. Lower Palisades Lake is busting with numerous and large trout. Should've spent more time here or else left myself enough time to hike down the steep slope at Upper Palisades since the trail crosses very high above the water there. To fish it would take more time than we had left in the day.
Lower Palisades Lake
Mather to Taboose/Pinchot - Great pools in the bottom of the valley that separates Mather and Taboose. My book recommended fighting up the brushy banks to Taboose, alas I didn't have daylight enough to make the effort.
Woods Creek to Rae Lakes - We were pressed for time, but these waters looked quite promising. One fisherman we met reported poor results. Hard to believe as the Rae Lakes were infested with hundreds of trout. At the crossing between Arrowhead and the lower Rae, literally hundreds of trout crowded a stream no more than two feet deep and eight feet wide. At upper Rae Lake, I couldn't fuss with a snack before a trout attacked my hopper in 8" of water two feet from shore.
Kearsarge Lakes - Our resupply detour to Kearsarge brought to more steady fishing. Lots of pressure here doesn't deter these trout. Alas, they seldom grow larger than 7"
Bubbs Creek to Center Basin - Some great looking waters here, big pools. Sadly, time didn't allow me to explore it much. In fact, I wouldn't drop a line again until Guitar Lake
Small Lake between Guitar and Arctic
Guitar Lake - Head up toward Arctic Lake and you'll find fun fishing waters at a small unnamed lake above the falls but just below Arctic. The trout were sluggish and more likely to nudge than take a fly so give them time to commit. The shores are shallow enough that you'll get one or two chances before all trout are spooked, but long casts into the middle won me a few decent strikes and some 9" goldens.