When the civil war broke out, Blake, in conformity with his avowed principles, declared for the parliament; and, thinking a bare declaration for right not all the duty of a good man, raised a troop of dragoons for his party, and appeared in the field with so much bravery, that he was, in a short time, advanced, without meeting any of those obstructions which he had encountered in the university. In 1645, he was governour of Tauntou, when the lord Goring came before it with an army of ten thousand men. The town was ill fortified, and unsupplied with almost every thing necessary for supporting a siege. The state of this garrison encouraged colonel Windham, who was acquainted with Blake, to propose a capitulation, which was rejected by Blake, with indignation and contempt; nor were either menaces or persuasions of any effect, for he maintained the place, under all its disadvantages, till the siege was raised by the parliament's army. He continued, on many other occasions, to give proofs of an insuperable courage, and a steadiness of resolution not to be shaken; and, as a proof of his firm adherence to the parliament, joined with the borough of Taunton, in returning thanks for their resolution to make no more addresses to the king. Yet was he so far from approving the death of Charles the first, that he made no scruple of declaring, that he would venture his life to save him, as willingly as he had done to serve the parliament. In February, 1648-9, he was made a commissioner of the navy, and appointed to serve on that element, for which he seems by nature to have been designed. He was soon afterwards sent in pursuit of prince Rupert, whom he shut up in the harbour of Kinsale, in Ireland, for several months, till want of provisions, and despair of relief, excited the prince to make a daring effort for his escape, by forcing through the parliament's fleet: this design he executed with his usual intrepidity, and succeeded in it, though with the loss of three ships. He was pursued by Blake to the coast of Portugal, where he was received into the Tagus, and treated with great distinction by the Portuguese.