I've done the San Marcos and the Comal many times. Both are very nice float dives, although you may sometimes feel silly floating in scuba in 5' of water as you pass over shallow spots. Still, I highly recommend them.
My dive club used to participate in the Comal River Trashfest each October. Sponsored by the Texas Gulf Coast Council of Dive Clubs (TGCC), participation was very high. During the fest, several hundred divers from area dive clubs would splash into the river in a massive post-season cleanup effort. It was a lot of fun and a very nice thing to do for the city of New Braunfels.
I don't know if they still do it, since I quit the club and quick diving for several years when my son became ill. I've since moved and haven't found a local club to join.
Back then, we would enter near downtown New Braunfels and work a section of the river real hard. We won the "tonnage" award 3 years straight. It was a great event, with an nice BBQ at the end and lots of neat door prizes.
Once, during Trashfest, my buddy saw a couple of workers toss a lawnmower into the river from a downtown bridge WHILE we were working that section of the Comal. He went over and tried to haul the mower out when he was accosted by the men who took it and threw it BACK in the river. In broken English, he was told "Deese ees OUR lawnmower. You put back. We put eet in reever, not geeve it to jew!".
We called the sheriff. He had a gun AND he spoke Spanish. Possession of the lawnmower was then a non-issue.
Both rivers are great for "treasure hunting" after pretty weekends. Drunken tubers lose a lot of stuff over the "falls" and in the "chutes".
Watch the currents in both rivers after a big rainfall. The chutes in the Comal can get dangerous, since all the water is trying to flow through a narrow spillway.
One winter, we decided to try a "warm" Comal dive, even though it had been raining for several days. We decided to start at a local German restaurant, and end at the "last stair" exit from the river where we left a car (be aware of the exit stairs. DON'T miss the last one, or you end up in the Quadalupe, in a BAD spot.).
Since our normal access was blocked off, we used ski ropes to "rappel" (well, sorta) down the nearly vertical riverbank for about 30 or 40 feet. At that point, there was no turning back, even when we realized the river was a lot faster and lot rougher when viewed up close.
I did the first chute headfirst and U/W, and it scared the beejeebers out of me. It was all I could do just to use my hands to fend me off passing boulders. But, overall the dive was very nice and the water was a comfortable 68 degrees.
The San Marcos river is home to the
rare "San Marcos Prawn". This huge crustacean (like a giant clawed shrimp or long crawfish) is only found in this river and in the Gulf, where it breeds. I understand (someone correct me), that it must go all the way downriver to the Guadalupe, then all the way to Gulf of Mexico for reproduction. After the fry hatch and settle the bottom they begin a long migration back to the San Marcos.
I think you can also see these prawns in Aquarena Springs.
Both rivers have a lot of Koi, mostly dumped from folks ponds and aquariums.
IMO, both rivers are fun places "do dives", but read this for a different opinion (ignore the guy's spelling, I like his style):
http://www.menet.umn.edu/~kaszeta/scuba/sites/txok.html
I have also tried the Guadalupe, but it is a tough river, with high currents. It is not a dive for the timid and there is usually less to see, since the vis is lower.