What is especially intriguing is Leonardo’s placement of vegetation in the picture, not simply to achieve aesthetic effect, but rather according to the location where such plants would grow. At the top of the grotto, the sandstone would have decomposed sufficiently to allow roots to take hold.  This is true for the plants growing in the foreground and in the background.  No plants are growing out of the diabase, however, since it is too hard and resistant to erosion to provide a suitable habitat for plant growth. (See details in Louvre version to the left and above).

Leonardo's Accurate Geology in Paintings and Drawings

An observer with some knowledge of geology would find that the rock formations represented in the National Gallery work do not correspond to nature, as do most of Leonardo’s drawings and paintings.  It seems unlikely that Leonardo would have violated his knowledge of geology, in favor of abstract representation, considering that he executed an even more geologically complex picture in the Virgin and St. Anne (1510,left photo), finished after the National Gallery painting.