I'm really not sure if I have to do anything with the patches in the water.
I cannot seem to get the last milk
You're right - the comment on the dark water was a red herring.
The last milk is the one in the shed? You probably need to get the milk in the hidden area. You can find it by walking through some of the trees in the area to the left of the one with the sign post. Come out of the house, go up through the garden to the main landscape with the sign post. Then left. You can walk through some of the trees in here.