Take the bus down to Agnew Meadows Campground and head out on the trail. This featured run takes you across the river to Devils Postpile
, then back across to go down the JMT toward Rainbow Falls (you can also stay on the Postpile side and go down to Rainbow). If you haven't been to Lower Rainbow Falls, be sure to go—the falls are different and beautiful and great for a swim. Once you are done enjoying the falls, run back up to the lowest bus-stop for the ride out.
There are a few water crossings, so you should have plenty of water with a filter.
The run starts on the Pacific Crest Trail with a bit of marsh and water crossings just out of Agnew—be prepared for mosquitoes for the first mile. At one mile, run down a shale-y switchback to the San Joaquin River.
After running along the river a while, there's a log crossing, then a really nice bridge that takes you to the west side of the river just before four miles in—at the Soda Springs junction. Just after 5 miles, there are some great waterfalls on the west side—you'll hear them more than see them. This is where Minaret Creek joins the San Joaquin.
Just after 5.5 miles, you'll be joining the JMT. Continue on parallel to the river, and you're in good shape. Shortly after—right around 6 miles—you'll come to a junction. The JMT/PCT continues, but I recommend you cross the river on a beautiful bridge and check out Devils Postpile
, then come back over after.
A couple miles later (exact distance depending on whether you toured around the Postpile), you'll cross the river again. Almost immediately, you'll have a junction for JMT/PCT or Rainbow Falls. Take Rainbow, of course. You should hit Rainbow Falls around 8-8.5 miles in. After photos and/or running down to the bottom of the falls (if it's open), head down to Lower Rainbow Falls—you've come this far, you've gotta go all the way!
After taking in the sights at Lower Rainbow Falls, follow the trail signs back to the lower parking area. There's a cut-off at one point for Red's Meadow that goes more east; stay toward the left/west branch or you'll have to come back down the hill to the parking area.