Villa de Leyva's historic centre is small and entirely walkable. The Plaza Mayor, the house museums, Casa Terracota, and the shops along Carrera 9 are all within ten minutes on foot of each other. Most visitors have no need of transport within the town itself.
To reach the archaeological and palaeontological sites outside town — El Fósil, El Infiernito, and the Convent of Ecce Homo — the options are taxi (negotiate a price for a circuit covering all three), bicycle rental (several shops in town hire bikes by the hour or day; the road is flat enough to be manageable), or on foot. The walk to El Infiernito is about 8 kilometres from the plaza; El Fósil is about 6 kilometres. Tour operators in town offer guided circuits by jeep, which is the most efficient way to see all three if you have limited time.
For Santuario Iguaque, take a shared minibus from the town centre to Arcabuco, then a local bus or taxi to the park entrance.