Many cars have separate reservoirs for brakes and clutch, but the e46 is not one of them. Bleed the entire system: if there is water in the clutch line, there will be water in the brake lines, too. Fresh fluid from each cylinder all the way to the top of the reservoir. It is only $10 and not difficult...just a hassle if you don't have a partner.
Just flush the fluid at least every 2 years (or whenever you do the brakes) and there shouldn't be any problem.