The first wing dam was constructed across the Des Moines River for use by the mills. Later, in 1846, a massive stone masonry lock and dam was built at Bonaparte as part of the Des Moines River Project, which was to enable navigation up and down the river. Part of the locks can still be seen in historic Riverfront Park.

When the river project fell through because of floods, the money and supplies were transferred to the railroad companies to enable the construction of railroads connecting Iowa towns. This construction had a positive impact on Bonaparte's industry and manufacturing, and unlike many river towns, Bonaparte continued to thrive. At its peak, Bonaparte had a population of almost 1,000 people.

In 1903, a major flood destroyed the dam and shortly afterward the Meek Mills were sold to pay debts. A major fire also occurred in the downtown area that year, destroying fourteen buildings on Main Street. Within a five-year period, the population dropped from 969 to 643 people. From this point on, Bonaparte stopped growing. The manufacturing and agricultural industries were no longer a powerful economic boost to the area.

In 1986, Bonaparte's downtown businesses were disappearing and the town was on the verge of dying. Several concerned individuals came together and developed Township Stores. They were able to restore many of the downtown buildings in keeping with the historic architecture, and enable several businesses to stay open.

With the help of government grants, the city park, downtown and residential housing have seen much improvement in the past several years.