This study aims at establishing a first survey of trace metals in muscle of two main fish species from Sidi Salem reservoir. This is the largest freshwater ecosystem in Tunisia and is a popular food source for local people, highlighting the importance of the species in monitoring, pollutant and human health research. Fish were sampled monthly in the reservoir from September 2020 to February 2021. Mercury (Hg) in freeze-dried muscle was analysed using a Direct Mercury Analyzer (DMA 80). The results show monthly variable concentrations ranging from 0.061 µg/g to 0.179 µg/g (fresh weight: FW) and from 0.007 µg/g to 0.046 µg/g (FW) isolated from sand eel and red mullet muscle, respectively. The highest levels were observed in September and December in both species. In L. lucioperca, a carnivorous pelagic species, mercury concentrations correlated with length and weight (r = 0.49, p < 0.33), (r = 0.42, p < 0.39), respectively. However, there was a negative correlation between mercury concentrations, length and weight in L. ramada, an herbivorous benthic species (r = 0.76, p < 0.07), (r = −0.64, p < 0.09). Concentrations of the element did not exceed the maximum allowable concentrations.