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While possible, it is quite unofficial. You will have to count on the generosity of a stranger from another crew, and luck to drive your vehicle, or shuttle you to fetch it. Having said that, it is a very common thing to do. You just have to make yourself known early to Brian (the race director), and to make the rounds of the other hundreds of paddlers and pit crews. In past years the race committee provided transport of camping gear, but no more.
If you haven't entered the 90 before, be sure to get your application in as soon as it comes out, usually around the 3rd week of June. Entry for newbies is by lottery. Last year the DEC allowed Brian to increase the number of entered boats from 250 to 275 for the first time. Even so, he had over 325 entry applications, and some had to be sadly turned away.
All of the lakes and rivers of the 90 miler allow motor boats and have many shoreline residences/camps. As a result, while generally "clean", I wouldn't call them exactly pristine. However water should not be a huge problem. Bring two or three of liters of water to begin, and there is additional water (and candy bars) available from race volunteers at several of the carries. Miles per day are approximately 35/30/25. Bring food to eat while paddling appropriate to your burn rate.
Some of us do the Cannonball-90, which is the entire traditional 90 mile course in a single day. All of it is paddled or carried without transport assistance, including a total of 10 miles of carries. It is not an official race, just something to do for training, usually around the time of the summer solstice for maximum daylight. Sometimes we have assistance with fresh supplies mid-way (at Long Lake), more often we are unsupported and bring all food and water (filtering or treating as needed) for the entire trip. I've done solo canoe alone, solo canoe with others, tandem canoe, and voyageur canoe. All fun.
It typically takes between 19-20 hours, depending on boat and crew. I really like to begin at exactly midnight in Old Forge.
After silently cruising past softly lit shoreline camps, paddling across the big lakes in total darkness by the light of the stars is not to be missed, especially if solo and alone. That schedule puts me on winding and often foggy Brown's Tract with just enough light to see for navigating the bends and beaver dams in morning dusk. The sun greets me rising over Raquette Lake while the water is still in morning calm. Arriving in Saranac Lake before sunset to a cheering small gathering is quite nice.
Note that the Yukon 1000 consists of a little over 6 days with max by the rules of 18 continuous hours (we keep it right to the minute) of paddling each day. With the current, average distance is 160 miles/day. The cannonball is good training.