An alien ship arrives (Rama like) at earth and issues an invitation to take people on board. They must be standing within so many feet of water at a certain time in order to go. They're told it's a one way trip I think, and are beamed(?) up.
I think it's set in contemporary time.
A scientist (a main character) goes with a military expedition. Once on board he later finds out that his daughter is also a passenger.
The ship has vast spaces inside, is sort of organic, and does turn out to be living. The travellers find that they are able to interact with the ship, they can create tunnels into the structure, persuade walls to grow from the floor, make the walls display colour.
They get a flu-like virus which kills some of them, but they realise afterwards that they now have no diseases at all, not even bad eyesight.
I believe they eventually find that they have become the ship's custodians and have to help it make the next ship for the next planet they visit.
EDIT. Added details. The daughter mentioned above is grown-up or late teens, the ship won't take children. She is 'adopted' on the ship by a group of feminists, and this makes it difficult for her father to find her, as they make their own little enclave.
The ship makes food, secretes it from the walls in certain places.
I read it possibly ten years ago. I have the feeling that it wasn't written any earlier than the 90's.