Many marine invertebrates have complex life histories that begin with a planktonic larval stage. Similar to other plankton, these larval invertebrates often possess protruding body extensions, but their function beyond predator deterrence is not well-documented. For example, the planktonic nauplii of crustaceans have spines. Using the epibiotic pedunculate barnacle Octolasmis spp., we investigated how the dorsal thoracic spine affects swimming and fluid disturbance by comparing nauplii with their spines partially removed against those with intact spines. Our motion analysis showed that amputated Octolasmis spp. swam slower, in jerkier trajectories, and were less efficient per stroke cycle than those with intact spines. Amputees showed alterations in limb beat pattern: larger beat amplitude, increased phase lag, and reduced contralateral symmetry. These changes might partially help increase propulsive force generation and streamline the flow, but were insufficient to restore full function. Particle image velocimetry further showed that amputees had a larger relative area of influence, implying elevated risk by rheotactic predator. Body extensions and their interactions with limb motion play important biomechanical roles in shaping larval performance, which likely influences the evolution of form.