Other improvements in the same period included sluices downstream towards St Ives and works to make the river navigable upstream to Bedford.
St Neots Manor passed from royal ownership under James I to Sir Sidney Montague. In the First Civil War, he supported the Royalist or Cavalier cause although his nephew, Edward, supported Parliament. As in most parts of the country, loyalties were mixed, but St Neots was firmly in Parliamentary hands and a detachment of Roundhead troops guarded the town. However, King Charles I passed through the town in 1645 and gathered willing recruits from local people.
On 10 July 1648 during the Second Civil War, a small battle took place when a group of 300 Royalists camped in the Market Square overnight. They were surprised and defeated by a smaller group of Roundheads advancing across the bridge, most of them being taken prisoner. A detailed account of the battle can be found in the entry for Henry Rich, 1st Earl of Holland, the leader of the captured Royalist force.
Many of the older buildings in St Neots and Eynesbury were constructed in the years following the Restoration of Charles II in 1660. There were 543 houses in the town in 1674 when records were taken for the Hearth Tax (though some of these may have been in nearby villages). Eynesbury Church was allowed to fall into disrepair during this period, until in 1684 the spire collapsed, causing serious and extensive damage. The building was repaired and the current tower built in 1687.