Water should be fine. I've done azide reductions, reductive aminations and benzyl hydrogenolyses in water, ethanol, ethanol/water mix, methanol, 1,4-dioxane, 1,4-dioxane/water mix, THF and ethyl acetate under H2 with 10% Pd/C. All work for those purposes (though I find ethyl acetate a bit slow).
What sort of hydrogenation are you doing, alkene -> alkane? Also, can you be more specific about the deviations?