In 1884 he became the city surveyor, in which capacity he oversaw the building of Seattle's first sewers and the Grant Street bridge across the Duwamish River tideflats. During the period when Thomson was city surveyor, he and Whitworth also offered their services in the private sector, maintaining an office on Main Street in what is now the Pioneer Square district. In 1886, he resigned to work for the Seattle, Lake Shore & Eastern railroad, for whom he plotted the route from the northern end of Lake Washington (now Kenmore) east through Snoqualmie Pass to Lake Keechelus. Before returning to become a consulting engineer in Seattle, he spent some time in Spokane, near the state's eastern border, where he was responsible for several railway terminals and two bridges. In at least 1890 and 1891, he worked for the then-separate city of Ballard (now part of Seattle), planning street improvements. As during his earlier work for Seattle, he continued at this time to work in the private sector, along with George F. Cotterill, who would soon work with Thomson for the city of Seattle and later go on to be Seattle's mayor. He applied in January 1891 for the job of King County surveyor. He was appointed in the position in May. However, after Edwin Hall Warner declined an appointment in May 1892 as Seattle city engineer, Thomson was again appointed to the city engineer position and resigned from his county position in July 1892. Thomson became Seattle city engineer in 1892, three years after the Great Seattle Fire had destroyed more than half of the city's downtown, followed immediately by an unprecedented construction boom. He began the process of paving roads, building sidewalks, and adding sewer lines (often through areas that earlier engineers could not work out how to plumb). With his assistant Cotterill, he laid out Lake Washington Boulevard, initially conceived as a path for bicycles. From the time of his arrival in Seattle, Thomson had considered the hilly landscape and the extensive mudflats as obstacles to the city's growth. He launched several regrading projects, most notably the extensive Denny Regrade, but also the Jackson regrade (between Main and Judkins Streets and 4th and 12th Avenues) and the regrading of Dearborn Street, with the 12th Avenue Bridge (now Jose P. Rizal Bridge) spanning Dearborn and connecting First Hill to Beacon Hill. He also drove Westlake Avenue through from Downtown to Lake Union, the first flat route connecting the two.