Estuarine sediments represent important pools of trace metals, released from both anthropogenic and natural sources. Fluctuations in the water column physicochemical conditions, on the other hand, may transfer metals from solid to liquid compartment and resulting in contamination of the surrounding environment. The present research was carried out to evaluate the weakly bounded heavy metal levels in tropical hypersaline and positive estuaries, in order to quantify its potentially availability. The monitoring includes five metals (Cd, Cr, Cu, Pb, Zn) and cover nine estuaries in Rio Grande do Norte state/Brazil, including four hypersaline and five true estuaries. 50 surface sediment samples were collected in each estuary. At the same time, organic matter concentrations were evaluated in order to help explaining possible local variations in heavy metal levels. Organic matter results (0.7% -7.3%) suggest the positive Potengi estuary as the most critical environmental quality situation. On the other hand, according to heavy metals levels, both Conchas and Potengi estuaries registered the higher concentrations of Cr. The highest concentrations were observed in the hyper-saline estuaries, with the exception of the Zn. The present study revealed that the watershed occupation has significantly influenced the heavy metal concentrations in the estuaries.