newts are super duper protected, you will proberly be tarred and feathered for cleaning the pond out without the paper work in place i would check to see which one of the two you have greater crested is the rarest by far. i would get on to one of the nature people at the council to get some advise, getting caught moving newts or killing them is a chargable offence, or you can keep your mouth shut and just be happy knowing that you are one of the very few, if you wake up one morning to find bill oddie in there thats your own fault just put him back where you found him
My view, for what it's worth is, I wouldn't want any nosey, peeping tom, civil servant type poking around my stuff.
It's the thin end of the wedge, what they don't see, won't overload their brain cell, and won't bring other civil servants from other departments, hell bent on stopping you from doing whatever you are doing, or putting constraints, and taxes, on you.
It also avoids unwanted publicity, and vandals, thieves etc.
If at some time in the future somebody in authority finds 'em, then that will be the first time that you will have seen them too, won't it?
Despite what the other posters have said I would get in touch with the local Wildlife Trusts - the council have no responsibility for wildlife and know naff all about it. Garden ponds are some of the last refuges for newts, frogs etc with the destruction of farm ponds that have gone on. There are 3 types of newt, common, palmate and crested. The crested newt is the one that is protected and is a magnificent little beast. If you had those in your pond you would be indeed very fortunate. i doubt whether anyone would prosecute because a) you were indeed innocent of their presence b) the newts probably weren't there if you did it early - they spend the winter on land under rocks etc, in my garden under pots in my greenhouse. In fact cleaning the pond may have improved things for them breeding for the next few years.
My understanding is that great cresteds need deeper water to breed in than the others so you are more likely to have the common.
The great crested is larger, about 6 inches long, black rather than green and has beautiful orange spots on the belly.
I know cause I handled one. I had never seen one until some kids at the school I taught called at the staffroom and plonked one in my hand that they had found on the tarmac playground. Not what you expect in the middle of a working day in December. So we went off to relocate it somewhere where the crows would not get it.
The Wildlife Trust would happily give you advice on encouraging them. In my case I got rid of my fish. They were boring whereas the newts, frogs, pond skaters, great diving beetles, dragonfly lavae were always up to something. Take a powerful torch down on a summer evening and the pond just comes alive with the wild stuff.