While most tenets of Neptunism were eventually set aside, Werner is remembered for his demonstration of chronological succession in rocks; for the zeal with which he infused his pupils; and for the impulse he thereby gave to the study of geology.

Within a year he published the first modern textbook on descriptive mineralogy, Von den äusserlichen Kennzeichen der Fossilien (On the External Characters of Fossils [or of Minerals]; 1774).

Socratic in his lecturing style, Werner developed an appreciation for the broader implications and interrelations of geology within his students, who provided an enthusiastic and attentive audience.

The emphasis on this initially universal ocean spawned the term "Neptunism" that became applied to the concept and it became virtually synonymous with Wernerian teaching, although Jean-Étienne Guettard in France actually originated the view.

How could he account for the covering of the entire Earth and then the shrinking of the ocean volume as the primitive and transitional mountains emerged and the secondary and tertiary deposits were formed?

The movement of a significant volume of water into the Earth's interior had been proposed by the classical Greek geographer Strabo, but it was not embraced by Werner because it was associated with conjecture.

[7] Among his most famous students was Alexander von Humboldt, who stayed in Freiberg in 1791-92, and initially subscribed to Werner's Neptunist ideas before departing from them in his later years.

[9] Werner’s major work, Von den äußerlichen Kennzeichen der Foßilien (1774), contained a comprehensive colour scheme he had devised for the description and classification of minerals.

The work, incorporating this colour nomenclature with some modifications, was translated into French by Claudine Guyton de Morveau (née Picardet) in 1790 and into English by Thomas Weaver in 1805.

Patrick Syme (1774–1845), painter to the Wernerian and Horticultural Societies of Edinburgh, published in 1814 a revised version, entitled Werner's Nomenclature of Colours, with Additions, arranged so as to render it useful to the Arts and Sciences.