This study evaluates the use of mercury (Hg) concentrations in fish muscle tissue to determine a species’ trophic position (TP) in its environment. A campaign conducted in 2019 along 375 km in the middle Araguaia River basin, Brazil, resulted in 239 organisms from 20 species collected. The highest total mercury (THg) concentrations were found in Pellonacastelnaeana (6.93 µg·g−1, wet weight) and in Triportheus elongatus (3.18 µg·g−1, wet weight), whose TPs were different according to the FishBase database. However, they occupied the same trophic level in this study. The intra-specific comparison showed a difference in Hg concentrations between individuals captured in distinct sites. The study of the biota–sediment accumulation factor (BSAF) showed that spatiality interferes with a species’ TP. Statistical analyses revealed that when we used a predicted species’ TP based on each individual’s size, it explained 72% of the variability in THg concentration across all fish species. Multiple regression analysis confirmed that standard length and FishBase values are positively associated with THg (R2 = 0.943). These results point to Hg as a viable indicator of a fish species’ TP since it reflects regional, biological, and environmental factors, as demonstrated here for the middle Araguaia River.