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Marine mammals possess impressive breath-holding capabilities made possible by physiological adjustments during dives. Studying marine mammals in their natural environment unravels vital information about these physiological adjustments particularly when we can monitor altered dive behavior in response to stressful situations such as human-induced oceanic disturbances, presence of predators and altered prey distributions. An important indicator of physiological status during submergence is the change in oxygen saturation in the muscles and blood of these mammals. In this work, we aim to investigate oxygen storage and consumption in the muscles of free-diving elephant seals when exposed to disturbances such as sonar or predator sounds while they are at sea. Optical oxygen sensors are a mature technology with multiple medical applications that provide a way to measure oxygenation changes in biological tissues in a minimally invasive manner. While these sensors are well calibrated and readily available for humans, they are still inadequate for marine mammals primarily due to a very small number of test candidates and therefore little data is available for validation and calibration. We propose a probe geometry and associated mathematical model for measuring muscle oxygenation in seals based on near infrared diffuse transport with no need for calibration. A prototype based on this concept has been designed and tested on humans and rats. We use the test results to discuss the advantages and limitations of the approach. We also detail the constraints on size, sensor location, electronics, light source properties and detector characteristics posed by the unique biology of seals.