While The Merlin Effect poses few if any controversial issues requiring social sensitivity, it does raise some philosophical and scientific questions which students may find interesting to discuss. Terry, Isabella, and Jim disagree on the best way to discover what is "true" and they each bring the methods of different disciplines to their work. Barron also raises the question of whether truth can be discovered not only through facts but also through faith. The research project team seeks to find and retrieve the wreck of a sunken galleon.

There is controversy in this field concerning whether remains of this type should be salvaged or left as graves. Finally, Kate's choice to rescue the whale, even though it causes the destruction of the research equipment, poses questions about the impact of scientific research on the environment.