A common technique for determining the mass accumulation rates of marine sediments is through measurements of constant flux proxies. These proxies, like unsupported 230Th and extraterrestrial 3He, are buried at a known rate at the seafloor, and thus their concentration in sediments is inversely proportional to the vertical mass accumulation rate of ambient sediments. These two proxies have varied assumptions regarding their behavior that have been difficult to test, particularly in regions of very low sedimentation. We present new measurements of helium and thorium isotopes in coretop sediments from the South Pacific Gyre. Our main finding is that 230Th- and 3He-derived mass accumulation rates of these sediments differ by a factor of 2–10, with 230Th-based mass accumulation rates systematically higher than those derived from 3He. While the final cause of the discrepancy is difficult to elucidate, we suggest that up to a factor of 2 worth of the sedimentary 230Th deficit can be explained by lateral transport of 230Th, while the remainder must be explained by other processes, such as ancient coretops undercorrected for post-depositional 230Th decay. Regardless of the mechanism, our findings have critical implications for the application of constant flux proxies in the South Pacific Gyre, with one example being the calibration of dust deposition models in this region. Ultimately, additional testing is required to determine the accuracy of the 3He and 230Th techniques for estimating sediment accumulation rates in regions of the open ocean with extremely low sedimentation rates.