The contract for the new station's construction was awarded to Jeremy Hixon Sr. and his son, and they arrived at Michigan City with a work crew and materials late that Spring. Over the summer of 1837, Hixon's crew erected a brick tower with a diameter of 14 feet 7 inches at the base, tapering to a diameter of 6' 11' below the gallery. With its massive walls tapering in thickness from 44' inches at the foundation to 28" in thickness at their uppermost, the tower was capped by a stone gallery floor, and an iron lantern with 18 glass panes on each of its eight sides erected at the gallery center. Capped by an iron pyramid roof with a copper ventilator, the lantern was outfitted with an array of four Lewis patent lamps equipped with 14" silvered reflectors. A short distance shoreward from the tower, a 1-½ story brick dwelling standing 34' by 20 feet in plan and containing five rooms was erected, and covered with a shingled roof. The dwelling was erected over a stone cellar in one end of which a plaster-lined brick cistern was installed to hold drinking water, either filled with rain water diverted from the roof or from water carried from the lake in buckets. A separate 14' by 16' summer kitchen erected a short distance behind the dwelling completed the station's complement of structures. To render the structures as visible as possible, all of the station structures were given multiple coats of whitewash, which was reported to be "dazzling in its whiteness." Edmund B Harrison was appointed as the first keeper of the Michigan City Lighthouse, and first appears in district payroll records at the station on September 12, and likely climbed the tower to exhibit the new light for the first time soon thereafter.

On November 3, of the following year, Lieutenant James To Homans, the Inspector of lights of the northwestern lakes, arrived in Michigan City, and found the station to be in good order, and carefully attended. However, the life of a lightkeeper was evidently not to Harrison's liking, as he resigned his position after four years to be replaced by James Towner on October 26, 1841. For reasons that have yet to be determined, Towner resigned in 1844, and was succeeded by his wife Harriet on March 21, 1844.

Little mention is made of the Michigan City Light station in government reports for the next five years until Superintendent Henry B Miller arrived at the station in 1849, and ordered that brickwork on the tower be re-pointed and the buildings re-coated with whitewash. Miller returned on July 22 of the following year, and observed that approximately half of the fence around station needed replacement as the posts were rotting. He also left materials and instructions to Mrs. Towner to have the shutters painted at a total cost not to exceed $10.00. With the formation of the new Lighthouse Board in 1853, one of the new Board's major initiatives was to replace all of the old Lewis Patent lamp systems with the far superior French Fresnel-style lens arrays. To this end, the Lewis lamps were removed from the lantern in 1857 and replaced by a fixed white Sixth Order Fresnel lens.

As was the case with most of the early Great Lakes lighthouses built under the Pleasonton Administration, the design, construction and materials used in building the Michigan City light were of low quality, and by 1858, it was clear that the old 1837 structure had deteriorated to a point that it no longer served as an effective aid to navigation to the increasing volume of maritime traffic seeking entry into Trail Creek, and plans were underway to replace the aging light with a new structure, Rather than incur the costs of undertaking a completely new design for the station, an existing set of plans were used, to which stations would also be built at Grand Traverse and Port Washington, among others. To this end, a work crew arrived at the station, and over the 1858 navigation season a 1-½ story dwelling standing 30 feet by 32 feet and containing seven rooms was erected over a full Joliet stone cellar. Centered at the north gable end of the shingled roof, a six-foot square white painted wood tower was erected and capped with a 6' diameter nine-sided iron lantern equipped with a new fixed white Fifth Order Fresnel lens which was visible for a distance of 15 miles in clear weather.

Three years after construction of the new building, Harriet E. Colfax was appointed as Keeper. Harriet was born in Ogdensburg, New York in 1824, and had moved to Michigan City with her brother in the early 1850's. Working as a teacher in one of the local schools, Harriet established a strong friendship with Miss Ann C Hartwell, who had also grown up in Ogdensburg and had also found employment as a teacher in Michigan City. Harriet's brother founded a local newspaper known as The Transcript, where Harriet soon ended up working as a typesetter. However, after her brother's failing health forced him to sell the Transcript, Harriet found herself out of work, and upon hearing that Keeper John Clarkson was resigning as keeper of the Michigan City Light, determined that she would seek appointment as Clarkson's replacement. A lady of petite stature, and by all accounts somewhat frail, Harriet appears to have been a person wholly unsuited to the hard working rigors of life as a light keeper. Thus, it is easy to speculate that her cousin Congressman Schuyler Colfax might have applied some political pressure to ensure Harriet's appointment as keeper on March 19, 1861. Regardless of the circumstances surrounding her appointment, Harriet quickly put to rest any concerns about her fitness for duty, and quickly proved herself to be a dedicated and hard working steward of the Michigan City light. With her responsibilities limited to tending the single building an light, Harriet was not provided with an assistant, however it appears that her longtime friend Ann Hartwell also took up residence in the lighthouse, and likely served to help with daily station chores.

By 1868, there were a number of leaks where the tower was integrated into the shingled roof, and the following year a crew arrived at the station to undertake the necessary repairs. Over the years, a number of squatters had moved onto the lighthouse property and erected ramshackle shacks in the area. It is likely that Colfax brought this to the attention of the District Inspector during his visits to the station, as the 1869 annual report contained a statement that "Measures should be taken to remove intruders who have settled upon the reservation."

By the 1870's it was clear that the short timber piers erected some 30 years previous were wholly unsuccessful, as even with frequent dredging, the depth across the bar at the river mouth was frequently reported to be as shallow as 2 ½ feet at times, with entry still blocked to vessels except those of the shallowest draft, and the Army Corps of Engineers again returned to Michigan City to begin extending the piers at the river mouth in 1871. To guide the way between the lengthened piers, a timber frame pierhead beacon was erected on the outer end of the east pier on November 20, 1871. With the increased workload resulting from responsibility for two lights at the station, Hayward Soloman was appointed as Harriet's assistant, reporting for duty on November 29.

In 1880, the dwelling and outbuildings were repaired, the tower and lantern were painted, and a 320-foot wooden fence was erected around the lighthouse grounds. Two years later, sand drifts, which had built up around the station buildings were leveled, and the fence on the north and west sides was replaced with a tight board fence to serve as a wind break to help stem future drifting. A well was dug and lined with brick and connected to a hand pump in the kitchen by an iron pipe.

While Colfax had likely appreciated the five assistants who had been assigned to the station to work with her over the past ten years, the assistant's position was abolished in 1882, likely as a district cost cutting measure, and Harriet was forced to make the grueling trip out to the pierhead light twice a night to tend the light.

By 1892, there had been little improvement in the situation with squatters on the lighthouse property, and measures were taken to evict them and their shanties were removed. Since the establishment of the original light 63 years previous, lamp oil had been stored in the cellar beneath the dwelling. However, with a change to the significantly more volatile kerosene, a number of devastating dwelling fires were experienced, and beginning late in the 1880's the Lighthouse Board began building separate oil storage buildings at all US light stations. To this end, a work crew and 6,000 bricks were delivered at the station in 1894, and a 350-gallon capacity brick oil storage building standing 7' by 12' in plan was erected 50 feet southeast of the dwelling.

With the Army Corps of Engineers engaged in constructing a breakwater on the east side of the river mouth in 1904, the Lighthouse Board began planning for the establishment of a combined first-class fog and light tower at its outer end in 1904. At 80 years of age, Harriet retired as keeper of the Michigan City Light after 43 years of faithful service to her station. Her love of the station is evident in her entry in the station log book on October 8 in which she wrote "Sold household effects preparatory to vacating dear old Lt. House." Thomas J. Armstrong, who had been serving as keeper of the South Manitou Light Station for the past ten years was transferred in as the station's new keeper, and Harriet departed her "dear" station on October 13, 1904. Harriet passed away five months later on April 16, 1905.

Simultaneous with construction of the new fog signal building, the old lighthouse building underwent considerable modification to convert it into a triplex dwelling, with 4 rooms for the head keeper and 3 rooms for each of his two assistants. As part of the reconfiguration, porches were added on each side of the building and the bricks of the upper floor were covered with dark green painted shingles. A coal shed and double privy were erected to the rear of the station and concrete walks poured to connect the station buildings. The Fifth Order lens was removed from the lantern on October 20, and reestablished in the lantern atop the new breakwater fog signal building, from whence it was first exhibited on the evening of October 20, 1904. No longer serving any purpose, the square wooden tower and lantern atop the dwelling were removed, and the building re-roofed.

With the creation of a city park around the harbor area in 1907, the Michigan City Board of Public Works received permission from the federal government to occupy and beautify most of the lighthouse property with the exception of the area immediately surrounding the dwelling. the After the US Coast Guard assumed responsibility for the nation's aids to navigation in 1939, crews assigned to operate the harbor lights and fog signal lived in the Coast Guard, with the old dwelling serving at times as a private dwelling and at times as a base of operations for the Michigan City Coast Guard Auxiliary. After sitting vacant for a number of years during which the venerable structure was significantly vandalized, the decision was made to excess the property in 1960.

The city purchased the building in 1963, and entered into an agreement with the Michigan City Historical Society in 1965 whereby the Society would restore the structure and maintain it as a museum. After eight years of restoration, the museum was opened on June 9, 1973, and since that date has remained opened to the public every summer, staffed by a dedicated group of Society volunteers.