Ontological naturalism extends methodological naturalism the rest of the way to encompass everything in existence, but restricts the knowledge to that already explored through methodological naturalism. Rather than being a method or process by which knowledge can be gained. It is a body of ideas which are known. Methodological naturalism provides the basis for the ideas held by the ontological naturalist. In other words, a natural historian can practice methodological naturalism and hold an ontologically naturalistic belief set. One who is strictly methodologically naturalistic will, of course, be an ontological naturalist. We can simplify these into more everyday terms to help further elucidate what is meant by them.
Natural History=the study of organisms in a wild context outside of a controlled laboratory
Methodological naturalism=Scientific and historical methods and similar epistemologies
Ontological naturalism=the belief that all observations have a material causation
I just heard some religious people say “AHA, naturalism is just a belief.” But this is intellectually dishonest, much as equating “theory” to “postulate or conjecture” as epitomized by “only a theory.” Ontological naturalism is epistemically grounded (one could almost say “encompassed within”) methodological naturalism, but this leaves a bit of a gap. While methodological naturalism includes ideas currently in the “testing, but somewhat supported” phase, ontological naturalism pushes them out into the “yet to be determined” category of information. While operating under methodological naturalism, one automatically assumes (at least for the purposes of the methodology and the duration of the work) ontological naturalism. In other words, methodological naturalism assumes ontological naturalism when it relates to the information itself. One that utilizes methodological naturalism as a tool for gaining new knowledge need not be strictly methodologically naturalistic, and thus, need not be ontologically naturalistic. If, however, someone is ontologically naturalistic, the are, necessarily, methodologically naturalistic.