Here's some pictures to give you an idea what we found. You want to stay in the channel on the San Pablo bay. It can be 5' of water in the channel and 3" outside the channel. Cross the bay on calm conditions. Incoming wind hitting an outgoing tide can be dangerous.
We were glued to our GPS, depth sounder and visual markers. The most shallow spot was out in the San Pablo bay. The river itself was approx 9' deep most of the way.
It's best to go up the Petaluma river on an incoming tide. If you run aground, you can wait for the tide to float you off.
Much of the way is no wake zones, especially near the little marinas. The river narrows near the town. You will come to the Petaluma Marina first. It is a nice little out of the way marina. From here you can take your dinghy up to the turning basin.
To enter the turning basin, you need to call the Petaluma visitors center to get hold of the bridge tender a day in advance. When he's done changing the oil on the city bus, he'll come down to raise the bridge for you. On the east side of the harbor is the commercial dock with various ancient fishing vessels. Above the commercial dock is the yellow house bar, which can be noisy.
On the West side of the turning basin is the downtown and Petaluma Yacht club. We enjoy being next to the city on this side. Above the dock is a decent coffee shop. Across the river is a decent brew pub eatery and excellent Italian restaurant.
North of the turning basin and slightly above the commercial dock is a food warehouse store. We stocked up on food at good prices there. I think last time we picked up French roast coffee for $3 a pound.
We would see an occasional tourist on the dock. Occasionally, the kids came down to the end of the dock to get high. They didn't seem interested in the boat at all. I saw one big boat move from the West side of the basin to the commercial dock to get away from the idlers. If security is a concern, then stay down at the marina and take the dinghy. I'm glad to read Kevfra's report that they have security gates now. We didn't have them when we were there.
Last year we got stuck at the city one night when the rains came in. We ended up taking the dinghy down the river to the marina in the rain. It wasn't that bad really.
All in all, it's a nice city to visit. The guides say to try Petaluma if the fog is thick on the SF bay. Petaluma is far enough inland to be warmer.