Soils and groundwater contamination modifies the physical–chemical conditions of the environment, altering natural biogeochemical processes of the ground. As a result, several mineral transformations occur, in which iron plays a decisive role. The presence of iron enables the study of magnetic properties, improving the understanding of the geophysical signatures of highly dynamic environments (e.g., biogeochemical hotspots and contamination plumes). In this work, we seek to identify creosote biodegradation related to the precipitation of magnetic minerals on sediments at a contaminated site in São Paulo, Brazil. Several rock magnetism analyses were carried out to provide the magnetic mineralogy of the samples in terms of their composition, size, and abundance. We conducted high-temperature thermomagnetic curves, frequency-dependent magnetic susceptibility, anesthetic remanent magnetization (ARM) and isothermal remanent magnetization (IRM) data, superparamagnetic concentration and dipole moment (SPCDM), and scanning electron microscopy (SEM) analyses. The magnetic signatures of the contaminated samples suggest an increase of superparamagnetic grains in the water table fluctuation zone if compared to the magnetic signatures of the uncontaminated samples. Thermomagnetic curves of contaminated samples showed a lower heterogeneity of the magnetic mineral phases than the uncontaminated ones. This work contributes to the advancement of the understanding of how natural biogeochemical processes are impacted by human actions, such as soil contamination, and even by climate change, which should affect soil redox conditions in periods of drought and flooding.