What are the best qualifications to have to become a Water Resource Engineer?

A thorough understanding of hydrology and hydraulics is essential to doing the job well. It will also benefit you to study spatial analysis in a class where you can practice using ArcGIS or QGis. If you major in Civil Engineering, you will be well qualified to be a water resources engineer. Other suitable majors include Environmental Engineering and Biological/Bioengineering (think food, water and energy engineering--not necessarily biomedical engineering).