Catedral de Sal, Zipaquirá Museum of Salt Works (page under construction)
Corals of Islas del Rosario National Park (ca. 20,000 ha offshore), see also here and here  
Cronosaurio "el fosil", Villa de Leyva, Boyaca
Gold Museum, Museo del Oro, Bogotá (>33,600 handcrafted gold objects); see also here   
Museo de Ciencias Naturales de la Salle, Bogotá
Museo de Historia Natural de la Universidad del Cauca, Caldas, Popayán; see also here and here  
Museo de Historia Natural de la Universidad Nacional, Bogotá
Museo del Mar, Universidad Jorge Tadeo Lozano, Bogotá; see also here  
Museo Virtual de los Minerales, Instituto Geofísico Universidad Javeriana, Bogotá; see also here  
Museums of Colombia (this page lists: Museum of Natural Sciences of Biffi-La Salle College,
    Iron Metallurgy Museum, Boyaca Fossils, Boyaca Museum of Natural History, Paleontology
    Museum of Colombia University, Geology Museum of Caldas University, Natural History
    Museum of  Cristo College, Natural History Museum of Cauco University, Cundinamarca
    Coal Museum, Zipaquirá Museum of Salt Works, Museum of Petroil Geology of Surcolombiana
    University, and Paleontological Museum in Villavieja, without further details).
Natural Sciences Museum, San Jose College, Medellín (rocks, minerals, fossils)
University Museum, Natural Sciences Division, Antioquia (minerals, fossils)