In 1689, the Calvert holdings at the northern end of the Chesapeake Bay were erected into Baltimore County, which originally encompassed much of the present-day counties of Cecil, Harford, and Baltimore City, as well as parts of Carroll, Anne Arundel, Howard, and Kent. In an area so vast, with a transportation network resembling Indian paths more than modern roads, it is not surprising that the early towns and county seats were located on navigable waterways. Baltimore County's first permanent county seat, known as "Old Baltimore," was located on the Bush River in what is now Harford County. It remains in dispute whether a town at "Foster's Neck" on the Gunpowder River existed before Joppa was laid out there, but by 1712 the legislature authorized that Joppa become the new county seat of Baltimore County.

Although the legislature had authorized the creation of Joppa, and it appears that certain settlers started to construct buildings near the site, it took another twelve years to straighten out the legal title to the future town site. By 1725 Colonel James Maxwell had agreed to sell twenty acres of the land grant "Taylor's Choice" for the creation of Joppa, and in 1726 Colonel John Dorsey surveyed the property, which was divided into forty lots of one-half acre each, a one-acre parcel for St. John's parish church and a site for the court house and jail. The lots sold for one pound, seven shillings each. It was mandated that each lot purchased should have a house containing no less than 400 square feet erected within one year of the purchase of the lot.

By 1750 Joppa consisted of some fifty houses, the church, a courthouse, three stone warehouses, stores, inns, a public wharf, a community well for drinking water, and a nearby race track. Joppa became a significant market place for tobacco and other agricultural staples, partly due to its access to the shipping trade and partly due to the government's incentive to bring tobacco to Joppa. During that era taxes were typically paid off with tobacco instead of currency, and a 10 percent reduction in the debt was granted if one brought the tobacco to Joppa. Certainly the annual elections and judicial proceedings at the courthouse also acted as drawing cards. During the 1750s and 1760s Joppa, along with Baltimore City, were the most active centers of commerce and social life in the northern Chesapeake region.

The introduction of flour mills along the Jones Falls ensured that Baltimore eclipsed Joppa as the center of the region, and by 1768 the legislature authorized the county seat to move from Joppa. Reports indicate that Joppa did not immediately fade into the shadows because the town was still active during the Revolutionary War. Yet by the 1780s the once bustling town was in decline, and larger ships found its anchorage unsuitable. By the 1800s only the remnants of Joppa were visible on the Harford County side of the Gunpowder River approximately a mile northwest of the railroad bridge over the river.