The Cocos plate experiences extensional faulting as it bends into the Middle American Trench (MAT) west of Nicaragua, which may lead to hydration of the subducting mantle. To estimate the along strike variations of volatile input from the Cocos plate into the subduction zone, we gathered marine seismic refraction data with the R/V Marcus Langseth along a 396 km long trench parallel transect offshore of Nicaragua and Costa Rica. Our inversion of crustal and mantle seismic phases shows two notable features in the deep structure of the Cocos plate: (1) Normal oceanic crust of 6 km thickness from the East Pacific Rise (EPR) lies offshore Nicaragua, but offshore central Costa Rica we find oceanic crust from the northern flank of the Cocos Nazca (CN) spreading center with more complex seismic velocity structure and a thickness of 10 km. We attribute the unusual seismic structure offshore Costa Rica to the midplate volcanism in the vicinity of the Galápagos hot spot. (2) A decrease in Cocos plate mantle seismic velocities from ∼7.9 km/s offshore Nicoya Peninsula to ∼6.9 km/s offshore central Nicaragua correlates well with the northward increase in the degree of crustal faulting outboard of the MAT. The negative seismic velocity anomaly reaches a depth of ∼12 km beneath the Moho offshore Nicaragua, which suggests that larger amounts of water are stored deep in the subducting mantle lithosphere than previously thought. If most of the mantle low velocity zone can be interpreted as serpentinization, the amount of water stored in the Cocos plate offshore central Nicaragua may be about 2.5 times larger than offshore Nicoya Peninsula. Hydration of oceanic lithosphere at deep sea trenches may be the most important mechanism for the transfer of aqueous fluids to volcanic arcs and the deeper mantle.