okay,
making the reflection is the easiest bit, I got my water image, and an image of the Burj Khalifa for this tutorial.
okay first, stick some decent music on, get those creative juices flowing.
second, open your water image, and paste the image to be reflected onto a new layer on top of that.
the blend mode you put the reflected image on can vary, depending on color, and how much of the reflection you want to see, with mine, I used Overlay.
it might prove beneficial to apply a small gaussain blur, you could add a displacement map too, but it could be getting more tricky than required.
okay, next the removal of some parts of the reflection.
you need to use a layer mask, if you don't know what one is, and how to use it, check
here
basically just paint anything you don't want to see black on the layer mask. it's that simple.
if you want some reflected but some opaque, duplicate the reflection layer, set the blend mode to normal, select the layer mask, and press cntrl/command+ I to invert the layer mask.
voila!
if this doesn't answer your question. lemme know and i'll try to figure something out.