Magnetotactic bacteria (MTB) are Gram-negative, ubiquitous, aquatic, flagellated, microaerophilic, or anaerobic microorganisms exhibiting magnetotactic behaviour based on magnetosomes, which are the structural signature of the group. Magnetosomes are ferrimagnetic nanocrystals surrounded by a lipid bilayer, usually aligned in chain(s) within the cell. Environmental abiotic conditions such as salinity, dissolved oxygen, pH, and oxidation-reduction potential may drive the diversity of MTB populations in environments. Our results reported the first evidence of MTB in sediments sampled from the Araguaia River floodplain in the Amazon-Cerrado biome. Light microscopy showed at least six morphotypes of South-seeking MTB. Transmission electron microscopy and energy-dispersive X-ray spectroscopy observations demonstrated magnetite cuboctahedral, prismatic, and anisotropic magnetosomes. PCA ordination demonstrated a more significant influence of depth, ORP (oxidation-reduction potential), and transparency in sampled data from the river main channel (MC). Non-metric multidimensional scaling (NMDS) ordination and correlation analysis demonstrated a difference between MTB populations inhabiting MC and lakes and affluent (LA). NGS and bioinformatic analysis revealed higher richness and diversity among magnetotactic cocci and the majority phylogenetic assignment of MTB affiliated to Pseudomonadota phylum. Hence, the complete acquisition of these results will provide further insight into magnetotaxis characterisation and the abiotic factors that impact MTB spatial distribution.