Couple of observations:

1. Tyler stop getting your water from the stream.

2. Personally I wouldn't choose this method because I think it causes banding in the remaining area, although if I did I'd have used the colour range command to select the blue area in my layer mask, saves a lot of manually brushing back in.

The way I would try is to duplicate the Blue Channel in the Channel Pallete.  Use the Curves on this channel to increase contrast. Control click on this channel to make a selection.  Use that selection to make a mask with whatever technigue you want to use to remove the dirt.  You would have to clean up the mask with White and Black but that is fast. Run a blur on the mask if needed. You could even use it on a layer with a color gradient, sampling that darker blue at the bottom and the lighter blue at the top.

This would not be the easiest way but as a tutorial it would introduce more concepts and possibilities.

Nice tutorial! I always perk up when I see "water" in the subject line. Because 75% of what I shoot is underwater (I do a lot of scuba-related work) I've dealt with bubbles and backscatter (caused by underwater strobes reflecting off particulate in the water.) I use kind of a similar method- I duplicate the layer, use the Noise>median filter until the backscatter is gone. Then in the history box I go back to LAYER VIA COPY, then I use the history brush, choose MEDIAN in the history window and set the history brush to DARKEN. Once this is done, I can paint over the backscatter areas and they're gone.

Andy

Well the water WAS pretty clean to start with, but after dunking fruit into it 50 or 100 times it gets pretty dirty

Yeah, I may of had some banding issues on these images - I think I solved that with adding some grain.

What method would you have used to clean up the water?

In regards to isolating the blue - I have never been very impressed by any sort of automatic isolation technique (when fine details are needed).  When isolating things I always end up using the pen tool or brush on a mask.  

Selecting the colour range is much more than just an automatic isolation technique, and can be used in many ways, in this instance once you'd done all your dust cleaning if you'd just selected the area containing the blue range of the water (fine tuned using the +/- and fuzziness tools) then you wouldn't have had to manually paint around all of the fruit because the fruit doesn't contain any of that colour range you've selected - if that makes sense which it probably doesn't.

I've just used this technique for a series of shots I did where my lights created huge highlights areas on the wall behind my subject, the walls were light green but so were other parts of the image, I selected the green range to only include the wall shades, then duplicated that selection and made it a uniform colour using the colour picker on an area of wall, then using separate layers with the opacity changed I added one as a 'darken' layer which gets rid of the highlights without effecting the rest of the wall including the area in between the guys hairs on his head, and I retain the shadows in the corner so it doesn't look like I've just painted in a new background.