We bike on the Erie Canal Path quite a bit. There are a few places that have access to water [some of the parks], but we always have our own water and fill up when we stop for a snack/restroom, so I can't be specific. Running from, say Fairport to Genesee Valley Park might be a nice run, but it might be a bit more than 16 miles out and back. Meridian Park [Brighton] and Perinton Park [Perinton] both have water, near the canal path.
Another place you might consider is the trail that goes along the Genesee River [west side], north of downtown, in the area of Holy Rosary cemetery/Riverside cemetery and up to Ontario Beach Park and then west along the Lake Ontario State Parkway and/or the road that runs along the lake, west of OBP [I'm having a brain cramp and can't remember the name!] or east through part of Durand Eastman Park along the lakefront. There is water/restrooms at OBP, for sure. All of this would be running on either paved paths or sidewalks.
I think you can find maps of these trails by doing a search on "Rochester Parks and Trails".