Human space exploration is expected to enter its next phase in the coming decades as the United States prepares to return to the Moon or perhaps venture even further with a crewed mission to a near-Earth asteroid. Both mission classes are viewed by NASA as precursors of eventual crewed missions to Mars. In anticipation of extensive robotic and human presence in the space environment beyond the protection of the Earth's magnetosphere, it is important to better quantify and bound effects of earthward directed solar storms not just on the human body but also on engineering signals. In this paper, we study the effects of solar storms on S band (∼2.3 GHz) radio links in the near-Earth environment, primarily for application to navigation. In particular, we are concerned with induced long-period signatures on Doppler tracking data that could be confused with the Earth's gravity signature, resulting in perturbed trajectory solutions of returning spacecraft during Earth entry targeting. We have quantified “worst-case” levels of such induced signatures on S band signal phase using model predictions based on measured in situ charged particle content from satellites and have compared these results with signatures seen in actual tracking data during periods of interplanetary coronal mass ejections (ICME) and related geomagnetic storms. We show that induced Doppler can mask Earth gravity field effects in navigation trajectory solutions at S band, a commonly used frequency for near-Earth communications and navigation. Finally, we suggest a few ways that such effects can be identified, alleviated or eliminated in near real-time.