After the Great fire of Hamburg of May 1842, he joined as a Secretary in the then formed Technical Commission for reconstruction, which included British engineer William Lindley.

Both Merck and his friend from Heidelberg University, Gustav Heinrich Kirchenpauer, were interested and they submitted their applications at precisely the same time.

[2] He was elected Syndicus replacing Karl Sieveking, joining Syndics Wilhelm Amsinck, Johann Kauffmann and Edward Banks.

Merck, who himself came from a wealthy merchant family, sought to guarantee the welfare of the city and its trade and promote the continuity of Hamburg's policy of neutrality and the preservation of its independence.

Merck's special position in the Senate can be measured by the fact that an exception was made in his case and he retained the title, rank and responsibilities.

[8][9] The three Hanseatic cities, through their joint envoy Friedrich Krüger, voted against the Austrian proposal and made a declaration (formulated by Lübeck) that the events in Holstein did not justify the mobilisation of Federal forces because the danger of an immediate collision had passed.

Merck learned more about Prussian intentions through diplomatic channels with the Hanseatic Minister-Resident in Berlin, Friedrich Geffcken, reporting that the Prussian Minister Alexander von Schleinitz said the King had stated that Prussia did not want to act against the Hanseatic cities, as they voted with Prussia in the Federal Diet on 14 June.

[10] The Lübeck Senate supported the Prussian view that the Confederation should no longer exist, because of the illegal action of mobilisation and proposed that their Federal Diet envoy Krüger be recalled.

Richthofen took part in this conference and emphasised that ending relations with Prussia's opponents was indispensable as a sign of friendly neutrality, and that therefore their Federal Diet envoy in Frankfurt, Krüger, must be recalled.

[10] Richthofen now tried to persuade the Senate of Hamburg to give in to other demands, to send a military contingent to help Prussia and to agree to a new federation.

The Hamburg Senate met on 22 June and approved the recall of Krüger, but, apparently encouraged by reassuring reports from Geffcken, decided to reject the Prussian alliance offer.

To soften the impression of rejection, Merck visited Richthofen on 23 June to inform him in advance of the result of the Senate meeting.

[11] Krüger, still their Federal Diet envoy, was not without influence on the decisions during the critical hours – he then returned to Frankfurt to make a joint statement on behalf of the Hanseatic cities.

[13] The day after the Austrian defeat at the Battle of Königgrätz, on 4 July, the Senate submitted to the Burgerschaft the following urgent requests: (i) Assent to the alliance with Prussia, subject to further negotiations on the details.

[14] On 18 August, Geffcken signed in Berlin a one-year duration treaty between Hamburg and Prussia, concluding an alliance to preserve the independence and integrity of their states.

[15] Merck, in addition to the Syndicate for Foreign Affairs, was given many other official functions, both in public and private, such as President of the Kunsthalle and the Hamburg City Hall Construction Commission, also chairman of the International Horticultural Exhibition of 1869.

He was spared seeing the occurrence Hamburg's absorption in the German Customs Union, the so-called “Zoll Anchluss”, as he died in October 1880 a few months before the conclusion of the treaty in 1881.