From The Mammoth Lakes area, there are three ways to get to Thousand Island Lakes. One is via the John Muir Trail. Another is via the River Trail. This hike description is the route via the High Trail, also known as the Pacific Crest Trail.
The High Trail officially starts at Agnew Meadows. From the trailhead, the trail heads up a series of switchbacks for about 400 vertical feet and continues to climb in a northwesterly direction once the switchbacks end until the trail tops out at about 9,700 feet. There are many small stream crossings during the first half of the hike and abundant wildflowers. There was lots of wild onion at all of the stream crossings when I hiked the trail. This stuff is quite tasty.
At this point the trail descends back down to about 9,540’ before continuing its climb toward the Badger Lakes. Shortly before reaching the Badger Lakes, the trail starts heading in a more westerly direction. Arriving at the first Badger Lake is a welcome sight because you are now only about a mile and a half from Thousand Island Lake.
From Badger Lakes the trail climbs steeply toward the high point of the trail to about 9,850. Along the way, the middle fork of the San Joaquin River is adjacent to the trail. Soon, the trail reaches a number of small linked ponds that are part of the outflow of Thousand Island Lake. This is where the Middle Fork of the San Joaquin River is still just a small stream. Here, Banner Peak is constantly in view due west.
At the high point of the trail you are greeted with your first view of Thousand Island Lake. The trail is fairly flat from this point all of the way to Thousand Island Lake. After approximately, 8.7 miles, the High Trail and The John Muir Trail intersect adjacent to Thousand Island Lake. This is quite a gathering place for hikers, but camping is not allowed near the outlet of the lake. Numerous campsite exist on both sides of the lake beyond about a quarter mile from the outlet.