We apply wave equation‐based techniques to 2‐D seismic data to characterize the nature of zero‐age upper crust at the East Pacific Rise from 9°16′ to 9°56′N. The final velocity model reveals a number of low‐velocity anomalies, complex in shape, extending down to ~1 km below the seafloor. We attribute them to the presence of hydrothermal flow. Depending on their spatial correlation with the previously identified tectonic discontinuities in bathymetry and presence of venting, we classify them as downgoing and upgoing pathways, respectively. This distinction is not always clear; within the third‐order discontinuities at 9°20′ and 9°37′N, both pathways may be present. The region north of 9°44′N, known for its magmatic robustness and volcanic activity, is represented by five low‐velocity perturbations. Three of these anomalies are spatially correlated with the fourth‐order discontinuities and attributed to the presence of the on‐axis recharge zones. The remaining two anomalies underlie two vent clusters, marked as hydrothermally active sites after the last documented eruption event. These velocity anomalies can be thus identified as the up‐flow pathways or at least their remnants. By comparing our results to the available interdisciplinary data sets, we show that the interaction between the tectono‐magmatic and hydrothermal processes is not straightforward due to different timescales at which they operate. However, for developing, maintaining, and driving vigorous, high‐temperature hydrothermal flow, the high crustal permeability and high thermal regime must coexist in time and space.