<p>Rapid urbanization in coastal cities has significantly increased the release of diverse toxic compounds via residential discharge. In the northeastern region of Rio de Janeiro, many pollutants, including persistent organic pollutants (POPs), hydrocarbons, permitted pesticides, and emerging contaminants (CEs), are systematically funneled into wastewater systems along rivers and channels from upstream areas to the estuary. Considering the hypothesis that contaminant accumulation in superficial sediments poses a risk to biodiversity, this study presents a detailed characterization of chemical groups at 29 sites along with the main water contributors to the Maricá Lagoon complex, revealing multifaceted contamination in both riverine and estuarine environments. Among the POPs, polycyclic aromatic hydrocarbons (PAHs) were detected at concentrations ranging from 216.45&#xa0;µg.kg⁻¹ to 2,166.6&#xa0;µg.kg⁻¹, which indicates moderate to high levels of hydrocarbon pollution in the region. Despite restrictions, organochlorine pesticides continue to be applied indiscriminately; for instance, dieldrin was recorded at concentrations between 0.87 and 4.48&#xa0;µg.kg⁻¹ — approximately 6.3 times above the legally allowed threshold—and hexachlorocyclohexane (HCH) levels surpassed permitted limits by a factor of 51. The evaluation of emerging contaminants highlighted that the transitional zone linking the channels to the lagoon was particularly impacted. In this area, Bisphenol-A was measured at 55.22&#xa0;µg.kg⁻¹, synthetic sterols at 748.05&#xa0;µg.kg⁻¹, and notably, contraceptive compounds at 730.88&#xa0;µg.kg⁻¹, levels that raise concerns over potential adverse effects on benthic organisms. Overall, these findings are essential to understanding the environmental repercussions of rapid urban transformation. They provide critical insights that can inform sustainable development strategies along with effective environmental management and conservation efforts within the Maricá Estuarine System.</p>