Repairing a wildlife stream and pond

[BertieFox]

We are really fortunate in having a natural spring which feeds a 'strong trickle' of water into a stream bed. Downstream we have dammed it to make a wildlife pond. Unfortunately, we have now discovered that most of the water in the stream is draining away into the bed and the pond has never been properly full since the first week or two after we constructed it. The pond has a proper membrane but the stream bed is not sealed.
Every time I start trying to work on this, I discover things like hibernating newts or frogs in the mud.
When would be the best time to carry out work on the stream bed without killing or harming the wild life? How do I 'seal' the junction between the stream bed and the liner for the pond? What do I use? The pond membrane is a plasticised material rather than being butyl.

[marchogaeth]

IMO whenever you do it you will upset something. At least if you do it in the late summer months things can usually run away which they can't if they are hibernating.

I'm no expert but it sounds like the membrane is the wrong thing for the job, couldn't you make a more natural shaped basin and puddle it in the deep part. If you've got good drainage you are working against nature, any natural expanse of water would be mostly boggy margins with only a fairly small deeper hollow in the middle. Good luck anyway.