A number of his original watercolours, however, are extant, including Fifty Flowers Drawn from Nature at Halifax (1785–1787) at the Natural History Museum,[4] an album from 1794 called "Twelve Posies Gathered in the Fields" held at Liverpool Museum,[5] and a collection of botanical paintings in the Lindley Library at the Royal Horticultural Society.

He also corresponded with many of the notable mycologists of his day, including Jean Bulliard, James Dickson, John Lightfoot, and Carl Willdenow.

The result was the publication of the first English-language work devoted to fungi, Bolton's three-volume An History of Fungusses growing about Halifax, published 1788–1790, with a supplement in 1791.

An additional album of 233 unpublished paintings of fungi, known as Icones fungorum circa Halifax nascentium, is held in the Special Collections Library of the United States Department of Agriculture.

A collection of 36 "fungi illustrations" (c. 1780) is also held at the Natural History Museum[4] and some additional sketches are in the library of the Earl of Derby at Knowsley Hall.

[10] Bolton's final published work was Harmonia ruralis, an "essay towards a natural history of British songbirds", issued in two volumes (1794–6).

[12] Bolton's fern and fungi books, with their descriptions of new species, remain of scientific value today, whilst his bird studies from Harmonia ruralis have retained their attraction – and have been reproduced as prints, on table mats and coasters,[13] and even on tea towels.