The ports in Stormhaven are old, and were important to the city long before Stormhaven became the defacto capital of Kildar. Initially small, and mostly used for commerce, they were greatly expanded at the request of the Navigators Guild during the Guild Golden Age.
The plan was to allow the Navigators' Guild to unparalleled authority over the newly built ports to more effectively combat the growing threat of the Anfyn Pirates. As a result, the docks would take on more of a military character and the entrance would be extensively fortified. At the forefront of the new renovations were the new barracks on the island in the bay, which would go on to serve as the main command post.
After the destruction of Torrica in 524, the Guilds needed a new place to convene and Stormhaven was selected as the new seat of the Landsraad. This brought new attention to the city, and over time the port would once more shift to focus more on commercial endeavors. As the city grew, and small ports were also increasingly used for intra-city transit, as some of the streets were found to be unsuitable to handling the ever-growing needs to handle the traffic of the ever-growing metropolis.
Traditionally, the port has been managed by the Navigators Guild ever since the expansions in the Guild Golden Age, though with the influence of the guilds waning and the importance of Stormhaven rising evermore, that arrangement is growing ever more uncomfortable.
Tensions flared when the Navigators' Guild tried to leverage their influence over the ports to coerce the council into closing the local portal by closing the small ports for intra-city transport. The city council initially tried to reach a compromise, but to no avail. After some vicious litigation it was eventually ruled that the Navigators' authority only extends to the ports that were in place during the Guild Golden Age. Other ports were to be sold off - mostly to the Inquisition - to prevent any single organization from holding such a chokehold over the city's commerce again.
Since then the ports have been split; between old and new; military and commercial; Navigator and Inquisition. The Navigators' Guild remains the most influential party in the docks, though they are no longer the only one.