Yups, it sounds very much like water lily root rot, one of the few
things which can destroy hardy water lilies, besides high salt levels

To stand some chance of eliminating the condition, empty pond, burn all
soil and plants, rinse all surfaces with a strong bleach solution (a
couple of times to be sure)

Alas, when folk find their waterlilies are disappointing (infected)
it's not unusual to find they dump them free on anyone who will take
them. Needless to say, unscrupulous folk slice them and dice them to
make a fast buck

To stand some chance of getting a water lily in good condition, take
care to get them from folk who have abundantly flowering collections,
odds on the owner knows how to keep their collection disease free.
Abundant flowering does not happen on infected ponds, with the
exception of just a few vigorous growing varieties

A few varieties can outpace the fungus, think twice about anything from
ponds where only Alba, Attraction or Colorado's are growing...

Take care to examine any new plants before putting them in your pond
and apply harsh bleach disinfection... I've come across infected
rhisomes inserted into the soil of marginal plant pots.

It seems some folk are determined to infect our ponds to increase their
chances of selling 'more' water lilies or 'pushing' tropical water
lilies onto the market as a solution to 'ponds where hardies don't
grow'

Regards, andy
http://www.members.aol.com/abdavisnc/swglist.html
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wrote:

Googling for Lily problems I found mention of root rot a fungal
disease. Does this sound like what I've got and if so what steps can I
take to prevent it happening again.

haven't tested it but the fish are all fine. Is there any levels ie
salt nitrates ph etc that would kill lilies.
Iain