In 1842 Henry stood as a candidate in the first Town Council elections in Melbourne. The election on 1 December 'was a wildly exciting and keenly contested one'. There were four wards, each with a polling booth in a local hotel. The polling for Lonsdale ward was held at the Royal Hotel in Collins Street and those elected were John Orr, Henry William Mortimer and John Pascoe Fawkner.²⁵ On 9 December the Council met at the Royal Hotel and, behind closed doors, voted for a mayor and four aldermen. In a close election, Henry Condell was chosen as the first Mayor of Melbourne. Henry William Mortimer was one of two aldermen elected for a three-year term.²⁶

'Garryowen' reported in his Chronicles that Henry was 'intelligent and conscientious, but had a precise and pragmatical mannerism, which prevented him from becoming popular', and that he retired from the Corporation 'to take part in the management of the Patriot newspaper'. Henry was one the 'chief projectors' of the Victoria Fire and Marine Insurance Company when it was established in October 1848 with capital of £100 000 in 4000 £25 shares.²⁷

Henry was interested in church-building and collected a large sum towards the erection of the Baptist Church in Collins Street. Along with Robert Kerr and John Lush he also started the first school for Aborigines at Merri Creek in 1846.²⁸ He 'had a good deal to do in the securing of Mr. Ham's [a Baptist Minister] valuable services, and though an Independent himself, Mr. Mortimer's energy and liberality on behalf of the early Baptists were as remarkable as creditable to him'.²⁹ Henry and Mary Mortimer were accepted into the Independent Church, St Michael's Collins Street, on 4 February 1852.³⁰

In 1863, when Dr John Dunmore Lang arrived in Melbourne, Henry 'in a few brief, stilted but suitable observations, officiated as the proxy of the ladies, and presented the guest with a minister's elaborately finished gown'.³¹ In 1864 he applied for the position of Deputy Registrar for Collingwood, using references supplied to him for his previous position, that of Inspector of Weights and Measures for the municipality of Fitzroy. In his application he said that

I am an Old colonist of some twenty five years and can refer to most of the men of influence here to say that I have an unblemished character. I have made a considerable fortune but lost it by becoming security for others and in the depreciation of property. At present I am Inspector of Weights and Measures for Fitzroy but the income of £5.18.0 per quarter is too small to live on. If the two positions are incompatible I will gladly resign the former.³²

Henry William Mortimer was listed as a new insolvent in 1861. The cause was given as his inability to meet his responsibilities and the depreciation in the value of freehold property. His liabilities were £13 394, his assets £16 995 and the surplus £3601.³³ His testimonials show that he was greatly respected and was indeed of an irreproachable and unblemished character. His integrity, energy and general business habits, over a long period in the history of the colony, were remembered, and the first person to sign the testimonial was John Pascoe Fawkner.³⁴