Understanding the significance that cultural ecosystem services (CES) have for traditional communities will provide useful input to the design of more appropriate regional or territorial plans for the area in which they are located. We conducted semi-structured surveys in 11 indigenous communities within the corregimiento La Pedrera, of the Colombian Amazon. We analysed the CES established in the region through a study of their preferences in relation to the service providing units (SPU) identified, using the Shannon diversity index method as an indicator of “diversity of use”. More CES were identified in communities with a larger population; Education and Recreation were the two most prevalent CES categories in the study area. Our findings also highlight the cultural importance of bodies of water, which were strongly linked with Spiritual and Sense of Place CES. Furthermore, the integration of qualitative and quantitative assessments enables a better understanding of the importance CES have for the local communities involved in the study and may assist in the management of the indigenous territory.