I tried simply animating the lake water but you can notice the outer edges slightly moving which in turn creates these fine noticeable lines.
You will need to use a mask to place in front of the water. This can be your existing background image with a transparent hole in it where you want the water to be and the water is then the watery part of that same image that you "cut" out of the original background. You then slightly enlarge the image of the water so that it overlaps the hole. You can do all of this using a single image which you include in the scene twice. The editing procedure in Gimp is
Load your original image
Add an alpha channel
Select the area of the image that corresponds to the water
Make the selected area transparent
Save using the option to retain colour information in transparent areas.
At step 4 be sure to use the option to "feather" the edges of the transparent area so that there are no hard edges to the "hole" that you are creating but instead the transition from opacity to transparency is gradual (but still rapid). Feathering is a setting that you can select on the tool you use to cut the hole in the image. You can also "touch up" an edge later by applying a blur to a region that is slightly larger than the hole or by running a blur tool manually along the edge to smooth off any "jaggies". If you do either of these use a magified view when doing the editing so that you have good control over the the area that is being acted on. In some cases a final touch up can be resorted to in which you use a high magification and manipuate the colour and opacity of individual pixels or small groups of pixels in order to eliminate ***** blemishes that for some reason catch your eye in an irritating way. I most often need to touch up edges in images created by others who have used simple "cookie cutter" tools to create hard edged holes, presumably cause they did no know about feathering or because a simple editing program did not have that as an option.
In the scene file you then display the background image twice - first as with 'blend: false' in order to be able to see the water which can be animated using a suitable shader and then with 'blend: true' so that you can see the water through the hole. But you display the first version with a scale factor of something like 1.1, 1.1, 1.0 so that it is slightly larger than the "hole" it goes in front of it. You may also need to slightly reposition it.
Now, because you want to have the boat be "in" the water rather rather than in front of it you need to use a slightly more complex method than the above, in particular you will need to use more layers in your scene - one for the water behind the boat, one for the boat, one for the water in front of the boat and one or more for the rest of the scenery. In this case you can't use the trick of using just one image displayed twice but will have to use several separate images each in their own file. These can all be copies of the same original image with different parts made to be transparent - that way you have no problems lining them up in the scene.
Actually, in this particular scene I don't think I would bother to animate the water, just gently rock the boat. But it is an interresting excercise that you might want to do it if only to learn how to do it. My "ReHa" scenes have a couple of "Small Pool" scenes that you might want to look at.
https://www.theemusnest.eu/scenes/Zips/TheEmu%20=%20ReHa.zip
Also in another scene that I am also working on I was wondering if I can change the background picture in a scene with another background picture while the scene is still active
Yes, I do that in quite a few of my scenes. Just animate the opacities to fade them in or out. The transitions can be fast or slow depending on what effect you want to achieve. See my "Tardis Conservatory" scenes for examples of this
https://www.theemusnest.eu/scenes/Zips/TheEmusTardisConservatory.zip
I also use it in my "transmats" scenes - though the transitions there are more heavily disguised. It is also used in a few of my "misc" scenes.