It is a pond's natural role in the scheme of things to fill in.
Try cutting them below the waterline.
The following are great resources
for large, natural ponds.
Earth Pond Sourcebook
by Tim Matson
and the newsgroup
misc.rural
and the ask the Pond Boss forum
http://www.pondboss.com/cgibin/ubbcgi/ultimatebb.cgi

good luck!
k30a