A 2003 interview in Newsweek quotes Stephenson's belief that "science fiction... is fiction in which ideas play an important part." Central to Quicksilver is the importance of the Enlightenment. By placing the reader among a world of ideas that change the course of science, Stephenson explores the development of the scientific method. One theme Stephenson explores in Quicksilver is the advancement of mathematical sciences which in turn led to important applications: Leibniz's theory of binary mathematics became the foundation upon which to develop computers. As he did in Cryptonomicon, Stephenson highlights the importance of networks and codes, which in Quicksilver occur against a "backdrop of staggering diversity and detail", writes Mark Sanderson in his review of the book for the Daily Telegraph. Also, returning to his cyberpunk roots, Stephenson emphasizes the manner in which information and ideas are dispersed in complex societies. Quicksilver uses the "interactions of philosophy, court intrigue, economics, wars, plagues and natural disasters" of the late 17th and early 18th century to create a historical backdrop. From one perspective, the characters are most useful in their roles as "carriers of information". Although the characters use various techniques to disseminate information, the most prominent is cryptography. Elizabeth Weisse writes in USA Today that the use of cryptography is "Stephenson's literary calling card", as she compares Quicksilver to Cryptonomicon.
In Quicksilver Stephenson presents the importance of freedom of thought, the diversity required for new ideas to develop, and the manner in which new ideas are expressed. To explore or accept an idea such as the theory of gravity often resulted in dire consequences or even "grotesque punishment" in the early 17th century. Stephenson also points out that research, particularly as conducted at the Royal Society, resulted in a changing of views in some cases:
If you read the records of the Royal Society and what they were doing in the 1660s, it's clear that at a certain point, some of these people – and I think Hooke was one of them – became a little bit disgusted with themselves and began excusing themselves when one of these vivisections was going to happen. I certainly don't think they turned into hardcore animal rights campaigners, or anything close to that, but I think after a while, they got a little bit sick of it and started to feel conflicted about what they were doing. So I've tried to show that ambivalence and complication in the book.
How to exist during a "time of dualities" is another important theme in Quicksilver, especially in their effects on Daniel Waterhouse, who is torn between "reason versus faith, freedom versus destiny, matter versus math."
Frequent mention of alchemy indicates the shift from an earlier age to a newer transformative age. Newton was an alchemist, and one character compares finance to alchemy: "all goods—silk, coins, shares in mines—lose their hard dull gross forms and liquefy, and give up their true nature, as ores in an alchemist's furnace sweat mercury". The book focuses on a period of social and scientific transmutations, expanding upon the symbolism of the book's title, Quicksilver, because it is a period in which the "principles governing transformation" are investigated and established. A commerce of different goods rapidly changing from one into another is a recurrent theme throughout the book. Also, the title Quicksilver connects the book to the method alchemists used to distill quicksilver, "the pure living essence of God's power and presence in the world", from, as one character put it, "the base, dark, cold, essentially fecal matter of which the world was made."