Should I keep a certain amount of the plant life and put it back in? - There is a healthy amount of frogs in one pond and Newts in the other, don't want to kill them off, so is there a "best" time of year to do the job? Any advice on protecting the little creatures appreciated!
I certainly agree with footprints that your best option is to reline with underlay (you can also use old carpet or sand for this) + butyl.
There is never a good time to do this sort of work on a pond, but winter time, when most pond critters are dormant, is the least disruptive. It's worth remembering that ponds are ephemeral features in nature and pond wildlife are good colonisers, so there's no great imperative to preserve the existing selection, but if you want to kick-start re-colonisation in the spring, keep a bucket of sludge from the bottom of the pond and reintroduce it when you've refilled.
If at all possible, refill with rainwater rather than tap water. Most tap water in the UK is contaminated with agricultural fertiliser, and this will inevitably cause excessive growth of algae in a newly filled pond, making the water cloudy and unsightly.
With respect to keeping plants, it depends on what varieties they are. If they're native species, then by all means keep them and use them again. If, on the other hand, they are non-native "ornamental" varieties, be aware that many of these have the potential to escape into the wild where they can cause serious ecological problems. If you have them, this would be the ideal opportunity to get rid (compost or burn) and re-stock with natives. More info here:
http://www.plantlife.org.uk/campaigns/INNS/
I'm assuming that your ponds are typical garden or fish ponds - deep, with steep sides. If you're keen on attracting wildlife, and you're going to the trouble of draining and re-lining anyway, you could also take the opportunity to re-contour the bottom of the ponds with sand to create shallower margins and planting pockets. The greatest bio-diversity occurs in water less than 10cm deep, and water over 1m deep is, effectively, ecologically sterile.
Plenty of info on wildlife ponds here:
http://publications.naturalengland.org.uk/publication/30031?category=430388
and here:
http://www.freshwaterhabitats.org.u...013/09/Creating-Garden-Ponds-for-Wildlife.pdf
This forum is also an excellent source of advice and info:
http://www.wildaboutbritain.co.uk/forums/
