Confluence has a nasty rep, but is bark is worse than its bite. Yes its urban, yes there are floating bottles and styrofoam, but whats a floating piece of foam going to do to you?
As noted above, the water quality is generally OK early season when its low like currently. I would avoid confluence immediately after the first storm flush, as every do turd in town will go into the river. After the flush (ie on the back side of the peak) I don't think the water is that bad, but the trash can be amazing (think 100+ bottles at trestle wave), but so can the surfing.
For what its worth, I regularly paddle at confluence, but I also live close by. Confluence always has water and it always has current to practice and get a workout. Its not going to win any awards for cleanliness or for beauty, but I know the 10+ early season training runs I put in pay dividends in May/June when the water hits. I see the same guys out there every weekend I go, and they say they have been paddling it for 15 yrs, and they are still alive.
So... if you want to get some training in, and don't mind some trash (that won't hurt you), then confluence is probably a good idea. If you get grossed out by floating styrofoam and can't handle it, then you might not like confluence.
Either way, its probably better off to judge for yourself.