the article refers to the museum next to the roundabout before the ras aboud flyover (at the end of the corniche). This is an old palace converted into a museum (for which the Aga Khan award was awarded). It had a nice little aquarium.
the whole museum has been closed and is "under renovation" for a few years now. I believe a much larger aquarium is proposed. u can actually see the existed lagoon there in google earth.