1. Parasites are an important part of ecosystems, playing a critical role in their equilibrium. However, the consequences of parasitism beyond the direct effects associated with disease and mortality are not completely understood. This gap in knowledge is in part due to the difficulties to isolate the effect of single parasite species on physiological and behavioral traits in natural systems. 2. The South American fur seal (Arctocephalus australis)-hookworm (Uncinaria sp.) interaction offers an ideal system to overcome these difficulties and study the behavioral and physiological effects of parasites in their hosts. 3. Hookworms cause stunted growth and anemia in pinniped pups, which could affect early life active behaviors such as swimming. The aim of this study was to determine the effects of hookworms (Uncinaria sp.). on the development of swimming capabilities in A. australis through physiological and ethological analyses. 4. Higher parasite burden was associated with reduced growth rates and lower blood hemoglobin concentrations, whereas scaled body mass and blood hemoglobin levels had an important positive effect on the water activity of the pups. However, anti-hookworm treatment did not affect the level of water activity of the pups, and pups with high hookworm burden increased their time budget in water. This was probably related to lower maternal attendance in heavily parasitized pups, leaving these pups more time to perform water activities. Therefore, pups with heavy hookworm burden, despite having decreased growth rates and blood hemoglobin concentrations, compensated for their handicap in physiological traits related to swimming by spending more time in the water. 5. This work offers new insights to understand the contrasting effects of parasites on aquatic organisms, and the compensatory mechanisms employed by infected animals to avoid the worst consequences of parasitism.