The Mundaú-Manguaba lagoon estuary complex is the most important ecosystem in the state of Alagoas, and a source of sustenance for a large number of the state’s inhabitants. However, degradation by anthropic sources has been causing impacts on this ecosystem. Understanding the characteristics of the natural organic material of the waters of the mundaú-manguaba lagoon complex is extremely important to understand the interaction dynamics of the contaminants in these lagoons. Thus, the objective of this work was to extract and characterize aquatic humic substances from the Mundau-Manguaba lagoon complex and to evaluate the interaction of this organic material with mercury ions. The profile of the aquatic humic substances of the respective lagoons evidenced the greater influence of aliphatic groups in their structures. The interactions of aquatic humic substances and mercury ions are directly related to the oxygen groups in their structures, corroborated by Principal Component Analysis. Thus, understanding the water and organic matter characteristics present in the Mundaú-Manguaba estuarine lagoon complex is fundamental for establishing strategies, seeking the preservation of this ecosystem and remediation of environmental contamination.