The loggerhead (Caretta caretta) is a cosmopolitan sea turtle species that are listed as vulnerable by IUCN and endangered in Brazil. In 2015, the C. caretta Southwest Atlantic subpopulation (SWA) was impacted by the Fundão dam break’ (FFDT) ore tailings plume and heavy metals, reaching the Espírito Santo coast (ES). The SWA is a great regional management unit (RMU) of C. caretta worldwide due to distinctive mtDNA lineage promoted by recent radiation within the Atlantic-Mediterranean region, however, due to the low resolution of mtDNA, the population structure of C. caretta SWA has been shallowly studied. Here, we recovered the genetic diversity and evaluated the population structure of the C. caretta SWA, using both mtDNA and 15 nDNA microsatellite loci, along with four nesting areas, and over 16 years enclosing the periods before and after the FFDT. We detected complex genetic dynamics that reflect on genetic composition at a population-individual level and revealed a spatial-temporal pattern that may be related to its philopatric behavior and relatedness. Further, we detected a genetic signature for the females of the ES nesting area that could be a consequence of recent demographic events and/or environmental responses. Thus, this study deeply evaluated the genetic diversity and provide a fine-scale resolution of the population structure of C. caretta SWA and the effects of environmental accidents (like the FFDT) on its life history. Lastly, for conservation purposes, continuous monitoring is needed to deeply evaluate if the FFDT has considerably impacted its evolutionary dynamics in the next generations.