A devout Presbyterian, this directly connected to others who shared his beliefs, and later became prominent supporters of Parliament, among them John Pym, Henry Darley, Lord Saye, and Lord Brooke. His second wife, Lady Anne Finch, was related to another influential Kent politician, the Earl of Winchilsea, and shared his religious beliefs. They purchased Winchester Castle in 1638, and lived a 'retired life' in the country, but as the political conflict between Charles and Parliament increased, Waller felt it his duty to participate. In April 1640, he was elected to the Short Parliament as Member of Parliament for Andover, then re-elected to the Long Parliament on 3 May 1642. A firm supporter of Parliament, when the First English Civil War began in August 1642, Waller was appointed a colonel, capturing Portsmouth, Farnham, Winchester and other key locations in southern England. At the beginning of 1643, Waller was promoted Major-general and placed in charge of operations in the region of Gloucester and Bristol. He was then called upon to oppose the advance of his old friend Sir Ralph Hopton, leader of the Royalist Western army, After the inconclusive Battle of Lansdowne on 5 July, Hopton linked up with Prince Maurice, and their combined force destroyed William Waller's Western Association army at Roundway Down on 13 July. The biggest Royalist success of the war, it secured the West Country, apart from isolated garrisons in Plymouth and elsewhere. Although defeat at Roundway had little impact on Waller's military reputation, there were increasing signs on all sides of war weariness, including anti-war demonstrations on 7 to 9 August in London. At a strategy meeting in Oxford, the Royalist high command agreed Prince Rupert would capture Gloucester, the last major Parliamentary position in the west, then move against London. This would be supported by Hopton advancing into Hampshire and Sussex, whose iron foundries were Parliament's main source of armaments. To counter this, Waller assembled a new army at Farnham Castle, consisting of Trained bands from the South-Eastern Association of Kent, Sussex and Hampshire, bolstered by others from London. Throughout the war, both sides relied on these militia; service was normally limited to 30 days, within their home area, but as the largest and best equipped, London units were often used by Parliament to fill gaps. Waller's army included several regiments mustered to repel Prince Rupert's advance on London, which ended at Newbury in late September.