For the sky you must get smthing called a "skymap" (https://www.wuala.com/Olson/Photos/Optikz_360_Skies/)
you have a skymap option in the rendering process (sky tab). You find your skymap in your folders and you open it, and then you change the sun azimut and altitude for the realism (you put the sun where the light comes). For the water i've done nothing (clear water and still water option must be disabled). I am not sure if it'll work, i am not a "professionnal" user of chunky but you can find many tutorial that could explain this tool much better than me.

Sorry if i misspelled smthing English is not my mother tongue :)

Thanks :)

That's not a shader mod, That's Chunky, a rendering tool for minecraft maps (http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-tools/1260564-chunky-minecraft-mapping-and-rendering-tool)