would the port facilities have generally been the same in the 17th C?
I really do not know much about sea passenger sailing in 17th c. But I know for the fact that passenger ships sailed on Polish rivers, especially Vistula. Not much is known about the way those ships were built but the richer the owner the more expensive the boat was. The King, lay and clergy magnates owned private boats.
The common people also used the passenger shipping. They were mostly trade people, brokers, agents and runners. In urgent trips they used small boats, taking up to 12 passengers. A journey from Warsaw to Gdansk lasted about 10 days. Including a few days of stay in the city - the round trip took almost 5 weeks.
Take a look at this - portgdansk.pl/en, and specifically at the history page of Gdańsk Port. See the first two images showing the congestion of ships in the Old Port. See how the ships are moored at the wharfs. As they say:
Likewise the traffic of ships was substantial considering that time.
Today, Gdansk's port is located in two areas: a so-called Inner Port is located at the mouth of Vistula River and the Outer Port - east of Vistula mouth, facing the Gulf of Gdańsk. There are numerous quys, piers and terminals there, including ferry terminals. See the interactive map here: portgdansk.pl/about-port/terminals-and-quays
The modern port has nothing in common with the historical port. No ships visit Motława river, with possible exception of Tall Ships and and the smaller yachts.
See for example this article and video in Polish, m.trojmiasto.pl/news/Zeglarska-parada-na-Motlawie-na-zakonczenie-Baltic-Sail-n59899.html from the Sailors' Parade on Motława, at the last day of Baltic Sail. See also some pictures here: balticsail.pl.
I have no proof that all the cargo loading took place on Motława. I am speculating here: the Vistula rafts would have hard time navigating upstream Motława, and they were possibly being offloaded (corn, wood, etc.) on the shores of Vistula.