I think one of the main themes is implicit in the book's title. When James asks his mother whether God is black or white, he is a boy living in a predominantly black community with a mother who looks white, and is simply expressing his personal confusion about race. To add to the confusion, however, his mother simply responds that she is "light-skinned". When his mother explains that God doesn't have a color, and that God is "the color of water", the image converges questions of racial and religious division into an essence that is clear and universally spiritual - in other words, "human". With all the intense stress of race, Ruth wants to instill in her kids that God has no preference for ethnicity or color of skin.