Facilities at El Refugio are simple but comfortable and adequate for basic scientific research. The station can accommodate up to eight researchers in two cabanas. Each cabana consists of two 4m X 4m bedrooms with two single beds each, a night table, shelves, chair, and clothing rack. Each cabana also has a 4m X 4m common room. In one cabana the common room houses a small library and research space with tables and desk lights. The kitchen is located in the other cabana. All buildings have lights provided by solar panels, and it is possible to connect computers and other electronic equipment to car batteries using a power inverter (one is available on site).

The shared kitchen consists of a table for eight, a gas stove with oven, a refrigerator with freezer, and a cold water tap. Cooking and kitchen utensils (pots, pans, plates, mugs, glasses, cutlery, etc.) are provided. As of September 2005, a bug-proof store will be stocked with basic supplies (dry goods, oil, canned food etc.), which will be available for purchase by researchers at market prices. It is recommended that researchers apply for a copy of the current list of goods available as their arrival date approaches. Researches should also bring their own food to supplement that which is in stock. Researchers will be responsible for their own meal preparation, however, it may be possible to purchase prepared meals on a per-meal basis when a cook is available. However, this cannot be guaranteed.

There are two restrooms. One restroom has a toilet, sink, and hot water shower, and the second restroom contains two separate toilets, two shower stalls (one with hot water), and three sinks. There is also an outdoor sink that can be used for washing clothes.

In addition to the shared lab space described above, there is an unscreened but roofed ambient lab available for scientific use. Current lab supplies are minimal so researchers should be prepared to bring their own lab equipment. There is a large amount of space available for long and short term storage of equipment.

The trail system at El Refugio provides access to the forest on the camp (western) side of the Rio Paragua. The system consists of approximately 10 kilometers of abandoned logging road and trails. Horse trails and a dirt track provide access to the pampa aguada on the eastern side of the river.

At the height of the dry season in August or September, El Refugio sends a large supply truck to the site overland. Researchers may arrange for transport of bulky equipment at this time, space permitting. Researchers may also make special arrangements with the administration to have materials prepared on site in anticipation of their arrival.

Station fees are US $10.00 per person per night, which includes access to the facilities described above, bedding (sheets, pillows, and blankets), housekeeping in the communal space, and gas for refrigerator, stove, and shower. Resident guides can provide limited field assistance, and canoes and horses are available to researchers. A shortwave radio provides communication within the region.