The Flour Mill and Eco-Museum is a modest but worthwhile stop beside the old Rec del Moli canal. It explains how water shaped Castello d'Empuries: not just as scenery, but as power for mills, irrigation for fields and a reason the town grew where it did.
The museum works best if you have already walked the old centre, because it connects the stones and canals outside with the everyday economy that supported the medieval town. It is not flashy, but it gives useful texture to a place that can otherwise be reduced to one large church.