Were there two prisons?

I used to think that Phillipe was kept in the Bastille the whole time, but when we see the prison he's rescued from, it's a dank fortress that looks like it's on the sea when the Three Musketeers have to take the boat to get him and then row back to a shore. When he's recaptured and placed in what is said to be the Bastille, it appears to be on land in close proximity to the city when the Musketeers go walking towards it and then Louis and his men arrive on horseback, which is more accurate since the Bastille was a fortress on land near Paris and not the coast. It also has nothing filthy and dank in there like we saw at the beginning and looks even cleaner. I try to understand how these two different places are the Bastille, especially since Louis tells Phillipe "back to the prison you will go and into the mask you hate".