muddy? as in actual mud? there shouldn't be any mud in the system... what are you using as grow medium and a gravel if any? if you're using hydroton and you just added it, it is normal for the system to be cloudy for a bit if it wasn't washed thoroughly.
Dear Philip Altmann
Personally, it does matter with the capability of your filtration systems. I don't know what types of filter you are running right now. Anyway, to give you some ideas, I would like to suggest you to use a clarifier or a swirl filter following by a fine screen filter tank.
How long has your system been running and what media are you using? As Michael said, if it is a new system then it may take a little time for solids to settle and so will be cloudy for a while.
Secondly, what is your fish density and your growbed volume? If you have too many fish, and not enough media to act as a filter for all their waste, then you will have excess solids (and ammonia, nitrites or nitrates) in your system.
For the filter - I would check your growbeds and fish density first because if you get those right then you should not really need any additional filtration - but I would add a simple swirl filter if you think necessary. These can be made reasonably easily from a big old waste bin, some piping and a little DIY imagination (or a quick google or YouTube search).
As before though, check the other things first because if you get those right then anything additional (and a further potential breakdown point) can probably be eliminated.
A little more details about the system and the exact nature of the problem would help people to give you a more coherent answer.
If it's a small system that is brand new and you just put your media in, even if it was rinsed, it could still take a week or so for the water to really clear depending on the nature of the dust.
It might help to put a sock or old cloth diaper to catch the dust from the flow and change it out to help remove the dust from the water.
If this isn't a new or tiny system and you are talking about something quite large, then a swirl filter or settlement tank might be in order.
Actually you haven't even told us what type of system, is it a media bed system or a raft system?
I would imagine that by muddy you mean brown and cloudy. This is more likely algae than mud. You need some type of mechanical filtration.