No, the two sentences do not mean the same thing. "Inherit" means to receive or take possession of something from someone else at the time of his or her death or to derive a certain quality from one's parents or ancestors. In the sentence you provide, it seems that the word "inherit" is being used to suggest that Waterman has mechanical abilities because an older relative had such capabilities and the aptitude for those same skills was passed to Waterman. In the second sentence, "natural" is used to mean that the mechanical abilities are skills that Waterman possesses without having to try very hard. He is able to perform mechanical tasks easily and without much difficulty.

Actually, neither is entirely correct. The first sentence suggests two people: Waterman, and a child/grandchild. "Him" is the person who inherited Waterman's talents. A talent is "a natural skill", so there's no reason to say that talents are natural. You could add the word "naturally" to another verb. For example, "Waterman’s mechanical talents developed naturally." (Meaning, without any extra training for example.)