could it be dirt? (probably mixed with a bit of pathogen)

Thanks for replying, No it cant be because I washed nearly all of it off there were only a few tiny specs left and ive had these plants in here for two days and the water turned from crystal clear to brown overnight. I think it maybe algae?

I understand. It wasn't a sarcastic question. I've seen peoples systems where they didn't was off the dirt. that is why i asked.
Can you post pictures? usually, algae is green and the water would have to be exposed to light for it to grow.
I've never seen it grow THAT fast.

diatoms?

Sorry Grizzman I did not mean for my post to come of as aggressive. Here is a link to my reservoir and roots in the net basket, there a bit hard to see. http://imgur.com/a/xpMRF

Here is a link that might be useful: cloudy water pics

I didn't think you were being aggressive. I just didn't want you to think I was being a smart aleck.
I have never seen anything like that in hydro. Only ever seen it in small pools in creeks.
You could try adding some hydrogen peroxide to the water and see if that kills whatever is growing. you may have to do it consistently for a while to ensure all the germs (bacteria, fungi, what not) are dead though.

I will add some hydrogen peroxide to see if it will clear up the water. My PH has shot up to 7.2-7.5 as well. I seem to also be having some root rot and slime issues so I think maybe I inadvertently introduced some fast growing fungus or bacteria from the soil into my system. I will keep you posted thanks for all the help.

Are you using Lava Rock as your Grow medium?

Yes, I am using a mix of red lava rock and river pebbles at the moment. I cleaned both thoroughly before placing them in my system and did a dry run for 1 week before I put the plants in without a problem. Two days after I put my plant in my water started turning brownish and foggy with some nasty looking organic brown stuff. Do you think it could be some type of pathogen introduced by the lava rock?

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Good call Nu2hydro. I missed that as the problem.

Yep Lava rock is famous for all kind of diseases.

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I never had any problems with my lava rock and all I did was rinse them and put into the system.
Since the problem didn't show up until after you put in the plants, it is more likely the soil the plants were in contained the unwanted bug.

I had no idea thanks a lot guys I ordered some hydroton which is what I should have done from the beginning. On a side note my plants are doing better they seem to be finally recovering. I can see new white roots coming out and the water also is clearer then before I think using hydrogen peroxide, increasing the water flow and using a rooting hormone have really helped in this.

Good point grizzman, I should have sterilized my setup and not used plants transplanted from dirt. I think these two probably contributed to my problem.

Just don't take the transplant from dirt issue as an absolute. I tend to start about 90% of my seeds in soil then transplant you just need to make sure you start with clean soil.

Did you ever figure this out I have my water mixed in a bin of clean water and it still does it can’t seem to figure it out