Suspension feeding is one of the most widespread feeding strategies among benthic organisms. However, natural feeding ecology and energetics of benthic suspension feeders are poorly known. The scarcity of field methods, apparatus and protocols that facilitate obtention of reliable in situ data has contributed to this lack of knowledge. A detailed description of an improved semi-closed recirculating system as well as the experimental set up is provided for the study of energetics in benthic suspension feeders. The system, completely submersible and surface-independent, allows us to assess oxygen concentration changes and feeding rates under natural conditions. Methodological examinations are conducted to investigate: a) the circulation of the water within the chamber; b) the time required for the flushing pump to entirely renew the volume of water of the incubation chambers; c) the behavior of the species within the chambers; d) the time of acclimation to the chamber conditions for the different species; e) the maximum decrease in oxygen concentration without affecting respiration rate; f) the time required to detect changes in concentration of the natural food sources. The system and experimental protocol is tested with species from three representative phyla, Porifera, Cnidaria and Tunicata.