I read this book about 10 years ago. I think it was part of a series but I don't know how many books there were in total.
It was about a boy that lived in England and his house backed onto a river. There was a tree in the garden that I think was somehow magical - I can't remember whether he could time travel using it, or put notes into it that would be available to people from different times in history? The boy used the tree to interact with his ancestors.
Maybe Robert Holdstock's Mythago Wood?
The protagonist is a boy in the beginning, and there is a stream/river on the grounds, which are next to a forest that connects to England's past. The book is the first of a series.
As children, the protagonist and his older brother launch a toy boat down the stream, which loops into the forest, and when it comes back, it is much changed and looks like it was on an extended river journey.
I don't remember any particular tree being used to communicate with the past, though, and the protagonist is an adult most of the time. He does think back to events from his childhood, though.
The novel Mythago Wood was expanded from a novella that basically covers the first third or so of the novel. That novella alone is probably a better fit to your description than the entire novel.
I'm not sure about this but could it be the Magic Tree House?
Now it's been a while since I read these books but I recall it was about a group of kids going to a tree house. The tree house was built by Merlin and they had to go to different times and complete "quests".
