Lower back pain is a musculoskeletal disorder that is commonly reported among warehouse workers due to the nature of the work environment and manual handling activities. The objective of this study was to assess the ergonomic risks among warehouse workers carrying out high shelf (HS) and low shelf (LS) binning processes. A questionnaire was used to determine the prevalence of musculoskeletal symptoms, while a marker-based motion capture (MoCap) system worksheet was used to record the participants’ motion and determine the action risk level. A total of 33% of the participants reported lower back pain in the past seven days, based on the Cornell Musculoskeletal Discomfort Questionnaire (CMDQ) results. Analysis of the body velocities showed that the HS binning process had four major velocity peaks, defined as the initial, lowering, lifting, and final phases. In comparison, the LS binning process had two major peaks defined, the crouching and rising phases. There were significant differences between the mean velocities of the workers for the HS binning process, indicating that the workers have different movement patterns with varying velocities.