Bowen was born in Brooklyn, New York, in 1856, and graduated from Brooklyn Polytechnic Institute. He then attended Yale University as a graduate student but he did not graduate with his class, he was awarded an honorary master's degree in 1903 from Yale University. In 1881, Herbert received an L.L.B. in law and political science from Columbia Law School. Bowen published several volumes of poetry.
Bowen married Augusta Floyd Yingut on 26 February 1895 at a high society wedding in New York performed by Roman Catholic archbishop Michael Corrigan. After divorce Bowen married second wife, Carolyn Mae Clegg (1877-1949).
After law school, Bowen practiced law in New York City specializing in international law. In 1895 he was appointed by President Grover Cleveland as the American consul-general at Barcelona, Spain, where he served until 1899, and then consul-general in Persia where he served from 1899 to 1901. Bowen was appointed by U.S. President Theodore Roosevelt as envoy extraordinary and minister plenipotentiary to Venezuela in 1901. After few days in Caracas burst the Libertadora Revolution a civil war, in which a coalition of regional caudillos headed by the wealthy banker Manuel Antonio Matos, allied with transnational corporations (New York & Bermúdez Company, Orinoco Steamship Company, the German Railway and the French Cable among others), tried to overthrow the president Cipriano Castro. In some battles Castro personally participated at command of the government troops, including the most important such as The siege of La Victoria in November, 1902, where with 6,500 men manages to defeat to the 14,000 revolutionaries who tried to take by force. One month later the Britain, Germany and Italy fleets imposed a naval blockade against Venezuela by over President Castro's refusal to pay external debts and damages suffered by European citizens in the recent failed Venezuelan civil war. In retaliation after naval bombardments of La Guaira and Puerto Cabello, Castro ordered put in jail all british, germans and italians inmigrants who lived in Venezuela. Bowen, as interim diplomatic representative of the European powers which had broken relations with Venezuela, negotiated the release of the foreign nationals. After that Castro assumed that the Monroe Doctrine would see the United States prevent European military intervention in American hemisphere, but at the time the president Theodore Roosevelt saw the Doctrine as concerning European seizure of territory, rather than intervention per se. Roosevelt also was concerned with the threat of penetration into the region by Germany. In this regard, on December 17, 1902, Rafael Lopez Baralt the Venezuelan Foreign Ministry requested the ambassador Bowen the intervention as arbitrator in the conflict. The Bombardment of Fort San Carlos, at the entrance of Maracaibo Lake, by german battleships Panther and Vineta had not been approved by the British commander Commodore Robert Archibald James Montgomerie, who had been warned by Admiralty after the Puerto Cabello bombardment of 13 December not to engage in such action without consulting London; the message was not passed to the German commander, who had been told previously to follow the English commander's lead. The incident caused considerable negative reaction in the United States against Germany. The Germans said that the Venezuelans fired first, which the British concurred with but declared the bombardment "unfortunate and inopportune" nonetheless. The German Foreign Office said that the Panther's attempted incursion into the lagoon of Maracaibo had been motivated by a desire to ensure the effective blockade of Maracaibo port, by preventing it from being supplied across the adjacent Colombian border.. After that, the president Roosevelt promoted an international arbitration in Washington triggered by increasingly negative British and American press reactions to the affair. The blockading nations agreed to a compromise, but maintained the blockade during negotiations. Subsequently the US president Roosevelt informed the German Ambassador that Admiral George Dewey had orders to be ready the Caribbean fleet to sail from Puerto Rico to Venezuela at an hour's notice.. Bowen as representative of Venezuela government discuss the details of refinancial the debt and signed the Washington Protocols in February 1903. This incident was a major driver of the Roosevelt Corollary and the subsequent U.S. Big Stick policy and Dollar Diplomacy in Latin America. When Bowen returned to Caracas in January 1904 he noticed Venezuela seemed more peaceful and secure. Castro would reassure him that United States-Venezuela relationships were at a high point. However, after the Castro regime delayed fulfilling the agreements stated in Washington Protocols which ended the Venezuelan debt crisis of 1902–03, Bowen lost confidence after verifying the contributions to rebels of U.S. firms The New York & Bermudez Company and Orinoco Steamship Company at the end of failed movement to overthrow Castro, the government demanded them compensation of 50 million bolivars, but as expected the companies refused to pay. After that Bowen was dismissed in 1905 for impropriety.