I had that problem before. I trimmed all the roots. It took a while for
them to recover. I won't do that again.

You could try dipping the roots in a diluted bleach solution. That should
kill the algae. After relocating the WH, I would use a stick to poke and
stir the roots. That would remove some trapped air from the roots. After a
few times, the roots would stay down like before.

Hank wrote:

HELP! All my WH have been choked to death by algae collecting on the
roots. The lettuce is still alive but not looking too good. The only
part of the VF not affected is the watercress. I was washing the roots
every day(what a pain) but forgot for three days.= rotten WH straight
to compost.
My water is clear .... some algae on sides ..... lots on
roots?????????
What can I do other than wash the roots every day? This is a new one
on me.

--
some photos of my little puddle
http://community.webshots.com/user/hankpage1