Located in one of the least investigated parts of South America, very little scientific research has been done at El Refugio. As such, there are many opportunities for 'new' research in the area. Preliminary surveys of prominent vertebrate groups (mammals, birds, amphibians and reptiles) have been conducted, but new species are being added to site lists every year. Probably the most interesting aspect of research at El Refugio is the possibility for comparative research among the different habitat types in the reserve. Surveys at El Refugio and the adjacent Parque Nacional Noel Kempff Mercado indicate particularly high levels of beta diversity (turnover in species richness among habitat types). While species richness in individual habitats in the region is not necessarily high compared to other Amazonian sites, total diversity across habitats is quite high.

Other research possibilities at El Refugio are:

Fire ecology/climate change: El Refugio is located in a climate and habitat transition zone. Therefore, the effects of climate change may be seen before they become manifest in other areas.

Individual species ecology: El Refugio has substantial populations of many large charismatic vertebrates (Giant Anteater, Marsh Deer, Maned Wolf, Giant River Otter, Jaguar). Because the landscape is more open and anthropogenic pressure is low, sampling may be easier here than at other sites.

Wetland ecology: Much of El Refugio is covered by seasonally-flooded grasslands similar to the Everglades of the United States and the Pantanal of Brazil. However, El Refugio has been subject to less anthropogenic disturbance, making it an ideal site for comparative wetland ecology research

Anyone interested in working at El Refugio should consult Conservation International's RAP Working Paper 10 for an overview of research in northeastern Bolivia.