Droughts are becoming more intense and frequent in the Brazilian semiarid because of El Niño and global climate changes. The Jaguaribe River estuary is a semiarid ecosystem that experiences a reduction in freshwater discharges due to droughts and river damming. The decrease in freshwater fluxes has increased metal availability through the water residence time increase in the Jaguaribe River estuary. Then, this study aimed to evaluate the dissolved organic matter quality and its interaction with metals in the Jaguaribe River estuary after a severe drought period. It was performed through carbon analyses, fluorescence spectroscopy, ultrafiltration technique, and determinations of metals by ICP-MS. Optical analysis showed that the dissolved organic carbon (DOC) was preponderantly composed of terrestrial-derived humic compounds, while the low ratio between the particulate organic carbon (POC) and chlorophyll-a indicated that POC was predominantly phytoplankton-derived. DOC and POC presented non-conservative removal during the estuarine mixing. DOM and dissolved elements were mostly distributed within the LMW fraction and presented a low percentage in the colloidal fraction. Li, Rb, Sr, Mo, and U showed conservative behavior, while Cu, Fe, Cr, and V had non-conservative behavior with a significant positive correlation with DOM, suggesting DOM as a relevant driver of metal availability at the Jaguaribe River estuary even during the rainy season.