Magnetic susceptibility (MS) of sediment and rock has been suggested as a tool to indicate changes in weathering patterns, source area, trace metals, and particle size, each of which may also provide a paleoclimate record. We test the utility of MS in recording previously documented climate changes within Holocene estuarine deposits from four bays along the Texas coast of the northwest Gulf of Mexico: Baffin, Copano, Corpus Christi, and Galveston Bays. MS analysis indicates three populations of anomalously high values: at or near the 8.2ka climatic event, during the mid-Holocene at 5.5–5.0ka, and at 3.6ka. MS measurements from Copano and Corpus Christi Bay cores suggest that the 8.2ka event may have been multiple events. Although the initial focus of this study was on the use of MS to record the 8.2ka event, the younger MS anomalies that correlate within the mid-Holocene are equally important and more pronounced for the use of MS as a paleoclimate proxy. The strong correlation of anomalies between 5.5–5.0ka within multiple cores suggests a regional response to environmental changes that affect the abundance of magnetic minerals in the bays. We use multiple analyses to attempt to determine the cause of the observed MS anomalies in the bays. Frequency-dependent MS indicates that the majority of measured samples, including the anomalies, have no biogenically produced ultrafine magnetite with the exception of anomalies at 8.5ka, 8.3ka, and 7.8ka in Copano Bay. Particle size of the sediment is compared with MS measurements from Baffin and Copano Bays suggesting a weak correlation between particle size and MS. Inductively coupled plasma spectrometry and x-ray fluorescence fail to indicate anomalous values correlating with the observed MS anomalies. Both methods probably lack the resolution to detect the minor differences needed to cause the observed changes in MS. X-ray diffraction analysis indicates the possibility of a minor increase in magnetite at an MS anomaly in the Corpus Christi Bay record which may be sufficient in causing the elevated MS. We present three explanations of climate-controlled MS for the anomalous intervals. (1) Accelerated sea-level rise decreased the orbital depth of waves on the bottom of the bays. As a result, the sedimentation rate increased due to a higher accommodation for deposition. Due to rapid deposition, the flooding surface preserved authigenic ferromagnetic minerals within a redox layer which deterred the cycle of Fe from one phase to another. (2) An influx of detrital magnetite/maghemite to the bays occurred due to flash flooding during arid periods. (3) The MS anomalies observed in the cores represent an increase in background magnetic material. Models (1), (2), and (3) apply to the anomalies near 8.2ka and only models (2) and (3) provide plausible explanations for the younger anomalies as there is no documentation of sea-level rise during those periods. Despite the uncertainties in the mechanisms behind the MS anomalies, the correlation of the climatic events within multiple bays along the Texas coast suggests that MS may provide a correlation tool within estuarine fills of the Gulf of Mexico Basin and perhaps across the globe.