In coordination compounds, the hydrate isomers differ in: 

The main difference between hydrate isomers in coordination compounds is the amount of water molecules used for hydration and the number of water molecules used as ligands.
Hydrate isomers are the isomers that result from the exchange of water molecules between the coordination and ionisation spheres. This phenomenon is hydrate isomerization.
The quantity of water molecules in the coordination sphere and ionisation sphere are consequently different for hydrate isomers.