The correct approach for the student to answer the question "How does the starting water temperature affect the time for the water to boil?" would be option D: Make the water temperature in each beaker different, heat the beakers equally, and measure the time for the water to boil.
This option allows the student to directly investigate how varying the starting water temperatures impacts the boiling time, which is the essence of the research question. The other options do not effectively isolate the variable of interest (starting water temperature) or introduce confounding variables.