I did this run as a part of a solo seakayaking trip based out of Stonington. I used my vintage Dagger Crossfire "race boat" and brought pretty minimal gear, camping at various Maine Island Trail Association sites around Isle au Haut.
After camping at the Kimball MITA site the night before, I paddled over to Isle au Haut village, filled up water at the NPS ranger station and took off on the Duck Harbor Trail, adding a spur down to the Loop Road where it came close, and then turning left onto the Bowditch Trail at the first junction. This took me over the high elevation point for the day, around 410'. I turned right at the junction for the Long Pond trail and went all the way down to the Loop Road before doubling back uphill and hitting the full loop down to Long Pond. There were some fun scramble-y downclimbing moves in this section! I had a quick stretch and swim in the pond before heading around the rest of the loop to the same Long Pond/Median Ridge trail junction, but this time I headed south, adding out-and-back spurs each direction on the Nat Merchant Trail, until I hit the Loop Road near the Goat Trail. I finished out the Median Ridge trail, then looped back along the Goat Trail (which was a little hard to follow) and down the southern coast to the Duck Harbor Mtn Trail. At this point I was out of water and the sun was out. The exposed scrambling over Duck Harbor Mountain was definitely the crux of the day. I decided to go all the way to the Duck Harbor campground water pump from there, where I took a break and rehydrated, before rolling back down the Western Head Road, doubling back to the Duck Harbor Mtn trailhead, and then finishing out the Western Head Trail loop. I hit the Duck Harbor pump again for more water before heading up the finishing Duck Harbor trail stretch north, adding a loop for Ebens Head (beautiful) and a spur for Deep Cove. Once I hit the loop road again, finishing the last stretch of trail, I decided to take the pavement back to the start, which started to bother my knees and was probably a mistake. I passed some of the park rangers as I was finishing up--they'd seen me heading out in the morning and asked which trails I did. "All of them, I think!" They were stoked.
I thought this ended up being a super accessible challenge--low vert and very runnable trails for the most part. The terrain was wonderfully varied, and I got to see so much of the island. My favorite parts were the swim in Long Pond, picking raspberries, and the sweet loam that kept my knees happy all day.
For gear, I kept it pretty light--a 0.5 liter softflask inside my Patagonia fanny pack with a few bars and a cookie, my iphone and a small external battery, sunglasses, bandana, and a mask of course. I wore my Altra trail runners. I wished I'd had some sunscreen, but I didn't end up catching much of a burn. No resupplies; two water fill-ups at the Duck Harbor campground.
The following day I circumnavigated Isle au Haut, took a nap on Kimball, and then paddled back to Stonington.