Archaeological evidence indicates that a smaller wooden and stone Norman church had existed on the location of the south aisle of the present building.

In this period there was change and upheaval across the continent and England following the arrests of the Knights Templar by King Philip the Fair of France on Friday, 13 October 1307.

Political turmoil from these events led to the Hundred Years' War and the eventual formation of the Church of England in the 16th century.

Foundation trouble, because of proximity to the river, delayed progress while the chancel was extended to prop the building up and create a greater level of structural stability.

Indicating the architectural skill employed by the builders at the time, the tower remains structurally solid and has not required any restoration work to realign it despite The Haven being only 33 feet (10 m) away and the original foundations built under water level.

A walkway at roughly two thirds of the height of the tower encircles the edges, giving great views from the Wash in the east toward Lincoln in the west.

The tower is topped with a highly decorated octagonal lantern ringed with pinnacles, one of fewer than half a dozen medieval examples surviving in England.

The relatively short period of construction for such a large church is fairly unusual in England, and an indication of the wealth of Boston.

Subject matter includes mythology, heraldry, and some everyday scenes - NB-02, for instance "Master seated birching a boy who is trying to protect himself with a book.

George Jebb's Guide to the Church of St Botolph, with Notes on the History of Boston mentions rings in the tower from which lights could be hung, pointing out that it was a popular practice.

Pishey Thompson, in The History and Antiquities of Boston, quotes from Britton, editor of The Lincolnshire Churches, in the Division of Holland: The lantern, no doubt, was intended to be lighted at night for a sea-mark.

The church of All Saints at York has a lantern very much resembling this of Boston; 'and tradition tells us that anciently a large lamp hung in it, which was lighted in the night time, as a mark for travellers to aim at, in this city.

The tower became important again in World War II, when Lincolnshire was known as "Bomber County" for its proliferation of air bases.

The yellow lighting of the octagonal lantern was specially put in place to represent the historic use as a marker to guide travellers on land and sea.

The spire of Harkness Tower at Yale University in New Haven, Connecticut (1921) and Riverside Church (1930) in New York City were the closest exemplars of the original masonry structure.

In what is still a matter of debate, there are a number of believed origins of this nickname that at first applied to the tower and is now frequently used to describe the whole church.

The third explanation is that it is named after the dramatic appearance it creates rising from the flat fenlands that surround it for miles.

The height of this above ground level is perhaps to protect the precious books contained within from flooding, an event that was frequent when the church was originally built.

The most notable titles are a 12th-century manuscript, St Augustine's Commentary on Genesis, and a 1542 edition of the works of Geoffrey Chaucer.

Some considered to be of political and religious importance were given by preacher Robert Sanderson, a royalist during the English Civil War.

The Parliamentary forces destroyed stained-glass windows that they found politically or religiously offensive, as happened in many other churches in Lincolnshire.

The changes they oversaw included the removal of the tower ceiling and the addition of stone vaulting, as originally featured in the medieval plans.

Artists who have performed at the church include Lesley Garrett, The Black Dyke Band, and The Pontarddulais Male Voice Choir.

On 26 June 2013, the Boston Stump Restoration Trust held their annual dinner in the nave in St Botolph's Church.

In September 2013, the Restoration Trust held a Grand Celebrity Concert with the St Botolph's Singers, featuring Caroline Trutz and Special Guest, Aled Jones.

The buttress on the south-west corner of the tower has been used since the 18th century for keeping a record of the heights and dates of flooding of the church by the River Witham.

The bottom pictures portray John Cotton witnessing the sailing of the Arbella in 1630, and Archbishop William Laud and Anthony Tuckney founding the library in 1634.

Some of Smith's pipes still survive in the present instrument but, over the years, various builders have had a hand in its development, namely Nicholls, Hill, Bishop, Brindley, Norman & Beard and Henry Willis.

In 1987, Harrisons carried out a restoration making some slight tonal changes and taking advantage of modern solid-state technology to increase the facilities.

In April 2007, they carried out some routine maintenance and cleaning, and upgraded the combination capture system to include 64 separate channels.