Although James Temple continued to be associated with the Thurrock area, Edward Whalley had fewer local connections. In 1636, Charles I levied the "ship money tax" as part of his effort to rule without Parliament. Henry and Edward paid the tax in Little Thurrock and "Mr Whalley" (probably Edward) paid in Chadwell; however in both parishes they were listed as outdwellers.

Edward also took a prominent part in the military action of the Civil War. He was in the skirmish at Gainsborough where his conduct was highly praised by his cousin Oliver Cromwell. He was promoted to Colonel and became part of Cromwell's new model army. He took part in the battle of Naseby and commanded the parliamentary forces at the siege of Banbury in 1646.

When Charles I was removed from the custody of the parliamentary commissioners, Edward Whalley and his regiment were given the task of guarding the King on behalf of the army. When the King's subsequently escaped from captivity Edward was left with with some explaining to do. On 13th November 1647, Colonel Whalley related to the House of Commons the circumstances of the King's escape from Hampton Court. He was ordered to present and sign a written account,[9] but appears not to have born the blame.

Edward returned to Essex during the brief royalist uprising in 1648. Parliament ordered Colonel Whalley "to pursue those that do continue in arms in Essex against the parliament". As a result, he was one of the commanders in the parliamentary army that besieged Colchester.[10]

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