The strategic picture in early summer 1645 was clear: the New Model Army had crushed Prince Rupert at Naseby on 14 June, and Lord Goring's Western Army was the last significant Royalist field force in the country. Fairfax pursued Goring into Somerset, linked up with Edward Massey's Western Association Army, and on 10 July destroyed the Royalist forces at Langport. Goring retreated through Bridgwater into Devon, leaving most of his artillery behind and a garrison of around 1,800 men under Sir Edmund Wyndham, the town's former MP. The path to Bristol now lay across the West Country. But Fairfax needed his rear secure first, which meant taking Bridgwater - an inland port on the River Parrett, ten miles from the sea at Bridgwater Bay, that had been a significant commercial centre and was now a Royalist stronghold.

Before he could besiege the town, Fairfax had to handle the Clubmen. These were local militia bands, often armed only with cudgels, who had organised across the West Country in self-defence against both armies. Many were hostile to whichever side had last requisitioned their food or trampled their crops. Royalist fugitives from Langport had been hunted down and killed by Somerset Clubmen in retaliation for earlier depredations. Fairfax met with their leaders and persuaded them that withholding support from the Royalists was the fastest way to end the war they all hated. They agreed to remain neutral in return for assurances that Parliament would pay for any supplies it took. The deal gave Fairfax breathing room to rest his troops and gather provisions before arriving at Bridgwater on 13 July.

Bridgwater straddled the River Parrett, with the main defences on the western bank including the old Bridgwater Castle - abandoned in the mid-16th century but with outer walls that, while not designed for artillery warfare, still presented serious obstacles. Wyndham's engineers had added earthwork batteries to the east mounting forty guns, with an additional battery between the west and north gates. The moat surrounding it all was filled by the tide at every cycle. Fairfax's first attempt, a night attack from the north on 14 July, failed when the storm parties discovered the water was too deep for their scaling ladders to reach the parapets from the bottom of the ditch. The next days were spent building siege works and considering a blockade. But Fairfax decided this was too slow. He planned a new assault.

On Monday 21 July, twelve hundred men were selected by lot - a deliberately random pick rather than ordering specific regiments forward into what everyone knew would be deadly work. They divided into a main party of 600 and two smaller parties of 400 and 200. At 2:00 a.m. Massey's guns opened fire from the south, and under the cover of that bombardment the storm parties crossed the Parrett on three pontoon bridges. Royalist fire from the castle was heavy but largely misdirected; the Parliamentarian casualties were lighter than expected at 20 dead and 100 wounded. The east gate was forced open, the main force poured in, and by midday they had taken 600 prisoners. The Royalists held only the western half of the town.

Much of the eastern section caught fire during the assault. Accounts vary as to who was responsible - whether the Royalist defenders set blazes to slow the attackers, or whether Parliamentarian incendiaries spread accidentally, or both. The garrison refused terms. A second assault was planned for Tuesday 22 July. By then it was clear the defenders had no realistic hope, and Fairfax allowed over 800 non-combatants - women, children, the elderly, the wounded - to leave the town under guard. Once they were clear, the Parliamentarian artillery began firing into the Royalist-held western section. It quickly caught fire too. By evening the burning was uncontrollable, and on Wednesday 23 July the garrison agreed to surrender. Around 1,600 prisoners were taken along with 40 pieces of artillery, powder, and a 'great store of musquets' that Goring had left behind.

By the etiquette of seventeenth-century siege warfare, a garrison that surrendered before its walls were breached was supposed to march out with possessions and a free pass to friendly territory. Bridgwater did not receive that courtesy. Most of the 1,500 rank-and-file soldiers switched sides and joined the New Model Army. More than 200 officers and Royalist officials were held prisoner. Sir Edmund Wyndham was kept in custody until 1649, when he joined Charles II in exile, returning only after the 1660 Restoration. The town itself was so badly damaged that economic recovery took decades. In December 1647, Fairfax himself wrote to Parliament asking that Bridgwater's taxes be reduced 'owing to its great losses in the recent siege.' Forty years later, in 1685, the Duke of Monmouth would make this same town his last headquarters before marching out to Sedgemoor - another rebellion against another king, another desperate gamble on the Levels, another defeat that would ruin many of the same families twice over.