On his return to Ireland, his father wanted him to find employment that would keep him in Ireland. He obtained the post of secretary to the
Commission of Prizes in 1664. Soon after, he married Elizabeth Dering (1649–1682), daughter of
Sir Edward Dering, 2nd Baronet, by whom his son
Edward Southwell was born. Her marriage portion of £1500 enabled him to buy one of the four clerkships of the
Privy Council. His linguistic abilities suited him for diplomatic service. He was appointed in November 1665 as an emissary to
Portugal, being knighted before he left. There he assisted in securing the peace between Spain and Portugal, which was achieved in February 1668. He returned to England, but was sent back to Portugal, staying for over another year. In October 1671, he was dispatched to
Brussels as
ambassador. On his return, he was elected to the English Parliament for
Penryn in 1673. He also took up again the post of secretary to the
Commission of Prizes, which he had resigned in 1667 and became his father's deputy as
Vice-Admiral of Munster. He also became a
Commissioner of Excise in 1671. Southwell was embarrassed by the
Popish Plot, being forced to testify at the trial of
Edward Colman that
Titus Oates, whom he detested, was telling the truth about the evidence he had given at a crucial Council meeting, and sold his clerkship of the Privy Council in 1679. However, he remained in favour, being appointed in spring 1680 as an envoy to the
Elector of Brandenburg, with the object of constructing an alliance against France. This took him to the courts of
the Prince of Orange and the
Duke of Brunswick–Lüneburg, but the project was no longer what
Charles II wanted. In 1685, he was elected to Parliament again, this time for
Lostwithiel. However, he was out of office in this period, having lost his Excise place in 1681. ==After the Glorious Revolution==