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In 2016, Brazil emitted 18.25 Tg of methane. Some of these emissions occur through continental aquatic ecosystems, locations of fate and accumulation of organic and inorganic matter. Thus, the aim of this study is to evaluate the origin of organic matter in Rodrigo de Freitas Lagoon, an eutrophic, coastal and chocked lagoon in Rio de Janeiro, Brazil, through the determination of n-alkanes and sterols compounds in the upper two centimeters of sediment and compare these data with methane ebullitive flux. The concentrations of n-alkanes varied between 2.43 and 25.82 µg g-1. C29 was predominant compound in most sites, but also with important petrogenic source evidenced by the occurrence of Unresolved Complex Misture. The total concentration of sterols ranged from 2.76 to 56.01 µg g-1. β-sitostanol was the most abundant compound and coprostanol was the most relevant at the sites under influence of domestic effluents. CH4 ebullitive flux averaged 199 mg m-2 d-1 in the dry period and 9.3 mg m-2 d-1 during the wet season. We conclude that the organic matter reaching Rodrigo de Freitas Lagoon through the rivers discharge added or enriched with irregular sewage input and petroleum derivates are the main source of eutrophication and generate higher methane emissions to the atmosphere.