Petaluma downtown is very walkable and ripe for creating your own routes, and Sonoma County is full of excellent parks for hiking. Putnam Park is one such park that's conveniently located in Petaluma.
There are gyms all over town, and quite a few in downtown including a 24 Hour Fitness.
The Petaluma Swim Center is a large pool that's great for lap swimming with a drop-in rate of $8. This winter they're open for lap swimming from 6 AM to 3 PM on Saturday and 8 AM to 3 PM on Sunday.