Scientist, teacher and writer, Johnson was associated actively with both the Franklin Institute and the Academy of Natural Sciences of Philadelphia. As educator, he was early concerned with better schools for instructing teachers and furthered the idea of free schools. His main interests were in the physical sciences, being a pioneer in studies of the properties of metal and coal. Geology also absorbed him and much of his later energies were devoted to that science. As a member of the Academy he served in several capacities; auditor, 1832-35; curator, 1835-37; member of the Publication Committee 1836-37; and corresponding secretary, 1841-48. He was chosen to deliver the address at the laying of the cornerstone of the Academy's new building in 1839. The original manuscript copy of this speech was recovered long years after, when the building was razed, from the cornerstone of the 1839 edifice, but meanwhile it had been published in the Proceedings.

Johnson was one of the founding members of the Association of American Geologists, which later became the Association of American Geologists and Naturalists. In Sept. 1847 this Association became the American Association for the Advancement of Science, and Johnson was elected the first secretary.