The operative word in Ross' reply is clean ...
A wet dirty bilge is a dark stagnant pond...a real "primordial soup." And it behaves like one, growing a variety of molds, fungi and bacteria—some that thrive in dark stagnant water, others that just like damp dark places. The warmer the weather and water, the faster they grow. Add some dead and decaying sea water micro-organisms, dirt, food particles, rain water, wash water, hot weather and humidity, plus a little oil or diesel, and you have a real primordial soup…no wonder it stinks!Most people’s approach to bilge cleaning consists only of throwing some bilge cleaner/and or bleach into that soup when it starts to stink and calling it done. I’ve never understood why they think that’s all there is to it. You wouldn’t just add some detergent or Borax to a bathtub full of dirty bath water or a sinkful of dirty dishwater, swish it around, then just pull the plug and expect the tub or sink to be clean without thoroughly rinsing it...so why would anyone think it’s possible to clean a bilge without rinsing all the dirty water out of it? Just pouring something into the bilge to try to kill off the "critters" that are growing in it is a waste of time, effort and cleaning product...'cuz unless you actually clean the whole bilge--every nook and cranny--and then flush ALL the dirty water out, the most that'll do is get rid of whatever is loose to go out the bilge pump. Any that are left will just multiply again into a smelly soup.The only cleaning product you really need is detergent and plenty of clean water. A power washer is the best tool for bilge cleaning 'cuz it gets detergent and then plenty of clean rinse water into all the places you can't reach by hand...and power washers require a LOT less elbow grease to accomplish a lot more than can be done manually. Clean your bilges, sumps and chain locker--really CLEAN 'em--once a year and you won't have to wonder whether you're starting any new life forms...and you'll be amazed at how much better your whole boat will smell.As for your fresh water system, search the archives for "Fresh Water Maintenance" (or check out the link below) for directions to recomission it. Do it annually as part of spring recommissioning to keep your fresh water tasting and smelling as good as any coming out of a faucet on land. If that doesn't suit you, install a filter. Just remember that a filter is in addition to system maintenance, not substitute for it.