In 1860, Walsh formed a decade-long partnership with James Smith. Prominent buildings from that period included Walsh´s revisions to St. Alphonsus Rock Church and the Four Courts Building at 12th and Clark Streets. By 1871, the Edmund Jungenfeld joined the firm. Smith left the office in 1874, the year of the final decision to build a new Post Office at the western edge of downtown. Local supervision of Alfred Bult Mullett´s design was given to Walsh, who was subsequently removed after being charged in the "St. Louis Custom House Ring," which had defrauded the federal government. Although Walsh and three assistants were indicted by a Federal Grand Jury in 1876, only two assistants were tried, and both were acquitted. The case against Walsh and one assistant was never brought to trial, but President Hayes removed Walsh from the job in 1878 and appointed Henry C. Issacs in his place.

Walsh continued to practice until his death in 1890. One of his final projects was the new campus for Saint Louis University, and the College´s Church.