Background <p>Brain aging leads to structural changes, especially atrophy, which can result in dysfunction. Mitochondrial dysfunction is thought to explain the structural changes in brain aging.</p> Objective <p>This study aimed to investigate the effects of a 12-week water-based resistance training (WBRT) program on brain structural integrity, mitochondrial-related growth factors, oxidative stress, and inflammation in older women.</p> Methods <p>A total of 24 older women (mean age:66) were randomly assigned to a WBRT group (<i>n</i> = 12) or a control (CON) group (<i>n</i> = 12). Participants in the WBRT group performed supervised resistance training in water three times per week for 12 weeks. Brain structural changes were assessed using magnetic resonance imaging (MRI), and blood samples were analyzed for Humanin (HN), Fibroblast Growth Factor 21 (FGF21), Growth Differentiation Factor 15 (GDF-15), Brain-Derived Neurotrophic Factor (BDNF), and Insulin-like Growth Factor 1 (IGF-1) as well as oxidative and inflammation biomarkers.</p> Results <p>The WBRT group showed significant increases in gray matter, subcortical gray matter, cerebellar gray matter volume, and cerebrum white matter compared to the CON group (<i>p</i> &lt; 0.05). Furthermore, WBRT resulted in significant increases in BDNF, IGF-1, FGF21, and GDF-15 levels (<i>p</i> &lt; 0.05). Malondialdehyde decreased, and glutathione peroxidase increased, with significant reductions in tumor necrosis factor-alpha and an increase in interleukin-10 in the WBRT group compared to the CON group (<i>p</i> &lt; 0.05), suggesting anti-inflammatory and antioxidant effects of WBRT.</p> Conclusion <p>These findings support the potential beneficial effects of WBRT as an non-pharmacological intervention to counteract age-related brain atrophy and promote brain health in aging populations.</p> Trial registration <p>IR.KMU.REC.1402.068, 29/06/2023</p>