Anthropogenic activities lead to environmental contamination with foreign substances such as heavy metals. This work was aimed to monitor trace elements (total arsenic (As), cadmium (Cd), chrome (Cr), cobalt (Co), copper (Cu), lead (Pb), manganese (Mn), mercury (Hg), nickel (Ni), and zinc (Zn)) contamination levels (dry weight base) in three natural freshwater reservoirs of Oman including Al Khawd and Al Amarat (Muscat Governorate) and Surur area (Ad Dakhiliyah Governorate as control area) using a native benthic inland fish (Garra shamal; Cyprinidae) for the first time. The muscle and liver of a hundred and twenty G. shamal were collected to assess the degree of metal contamination. Atomic absorption spectrometry was used as an analytical technique. From the spectrum of analyzed elements, we found Zn as a major element in monitored areas. The statistically significant (P < 0.05) highest concentrations of Zn liver (0.275 ± 0.065 µg/g) were in Al Amarat compared to the other areas. The concentrations of monitored elements in the fish muscle were lower than the liver samples. Furthermore, the fish length was significantly correlated with the accumulation of Hg and Co in both muscle and liver samples. In all analyzed fish from Oman inland water, the concentrations of elements were below the permissible limits; however, additional research is needed.