Sea fishing is one of the sectors with the highest risk of illness and work-related accidents. The purpose of the study is to evaluate the exposure of fishing workers to three major risks: biomechanical overload, noise, and whole-body vibrations. We used common methods and measurement tools in the field: observational video analysis, questionnaires, and direct measurement. Noise and vibrations levels were measured aboard five boats belonging to the main fishing communities of Southern Italy. The random sample consisted of 310 workers, of whom 108 agreed to complete a questionnaire to collect data on the perception of occupational risk and self-perception of health conditions. We found that fishermen had a high prevalence of osteoarticular pathologies (42%) and that the biomechanical overload risk is mainly related to handling manual loads. Furthermore, the results indicate that the levels of weekly noise exposure exceed the exposure limit value of 87 decibel A (dBA) for fishing workers, and that the most noisiest area is the engine room. Exposure levels to whole-body vibrations were below <0.5 m/s2. Knowledge on occupational hazards and health effects in the fisheries sector should be used to develop ship technology, raise awareness of the correct use of personal protective equipment, and improve health surveillance of these workers.