In many small-scale fisheries around the world, hookah diving is the main fishing method and gear to catch high-value species like sea urchin, sea cucumber, queen conch and spiny lobster. Decompression sickness (DCS) and carbon monoxide poisoning (COP) are diseases related to hookah diving and are the cause of non-fatal and fatal injuries in small-scale fishers with the social and economic effects over households and coastal communities. A misunderstanding about diving risks still prevails among small-scale fishers. This study reports on a qualitative risk analysis method developed to obtain fishers perception, the likelihood of undesired health threatening events occurring as a result of hookah diving, and the corresponding perceptions of impacts or consequences of such accidents. These risk perceptions are contrasted with hyperbaric physicians’ perceptions and the actual diving accidents occurring in the spiny lobster (P. argus) and sea cucumber (I. badionotus) small-scale fisheries in a Yucatan northeastern coastal community. Fishers identified the DCS as a major problem in the diving activity; however, their impact value perceived was lower than the one perceived by the physicians. Fishers diving behavior exceeded the recommended standards for a safety diving practice. The method allows for identification of priority decisions relevant to the need for appropriate fishing technologies, for fishers capacity building associated with health-related precautionary measures, and increased community awareness of possible consequences of current fishing technology.