There is an urgent need for healthcare research, funding, and infrastructure in the Peruvian Amazon. We performed a descriptive study of health, health knowledge and practice, and healthcare access of 13 remote communities of the Manatí and Amazon Rivers in northeastern Peru. Eighty-five adults attending a medical boat service were interviewed to collect data on socioeconomic position, health, diagnosed illnesses, pain, healthcare access, and traditional versus modern medicine use. In this setting, poverty and gender inequality were prevalent, and healthcare access was limited by long distances to the health post and long waiting times. There was a high burden of reported pain (mainly head and musculoskeletal) and chronic non-communicable diseases, such as hypertension (19%). Nearly all participants felt that they did not completely understand their diagnosed illnesses and wanted to know more. Participants preferred modern over traditional medicine, predominantly because of mistrust or lack of belief in traditional medicine. Our findings provide novel evidence concerning transitional health beliefs, hidden pain, and chronic non-communicable disease prevalence in marginalized communities of the Peruvian Amazon. Healthcare provision was limited by a breach between health education, knowledge, and access. Additional participatory research with similar rural populations is required to inform regional healthcare policy and decision-making.