The heights in this piece are more screwed up the more I look at them. ^.^;
There's wall height issues, discrepencies with the water heights (look at he bridges tot he right. They both have the same height of shadow, showing they're the same height above the water when the top on is on a higher level than the bottom one.) To fix this at least a little I'd add three tiles of height to the back wall where it meets the water (that 3 x 32 pixels). Then I'd drop the shadow of the top bridge down on or two more tiles and get rid of the raft altogether. (The wooden platform above the boat.) Then I'd add a 'drop off' to the right side where the houses are so that the bridge there is actually on the right height. As it stands things are really odd.
Also, the cutout part on the left doesn't fit. All you'd be able to see from that angle (supposing that the water is all one height) would be more wall.
A quick mock-up.
The easiest way to do heights is to set the bottom tile. In this case the water would be the lowest point. The highest is the wall. Each time you add a height make sure it's added all across the board. When you look at a part try and figure what tile height it would be. For example, in my mock-up the bottom most bridge is two tiles in height. Water = 0 and the two tiled walls are +2. The outer walls begin on +2 tiles and end at +6.
Or that the floor starts at 0, the wall takes it up to 4 and the water is at -2.
Hope this helps a bit and that I haven't gotten you all confused. ^.^;