Why would two isomers have different solubilities in water?
In the most general terms: Molecules consist of nuclei and a surrounding electron cloud. That cloud is dependent on molecular charge and geometry - so it will be different for two different isomers. It follows that its interaction with the nuclei and electron cloud of a third molecule, say, water, will be different. 

More specifically, one will find that properties such as 


polarizability (related to van-der-Waals forces)
bond dipoles (related to H-bonds and static dipole interactions)
effective electronegativity (related to H-bonds and static dipole interactions)


On a very basic level, any solvation involves the formation of solvent shells. When varying the shape and surface of the solute, those shells will change as well. One will then find shells that work well and others that work less well, influencing the solubility.