This work proposes a separation system that uses the Sep-Pak C-18 cartridge to enable the determination of labile and total lead in natural water samples. This method is composed of two steps. First, the sample is percolated through the cartridge, where the lead that is bound to the organic compounds is retained and the quantification of labile lead is performed using the eluate from this separation. Afterwards, another sample enables the determination of total lead. Lead was determined through electrothermal atomic absorption spectrometry (ET-AAS) using aluminum as a chemical modifier under the following instrumental conditions: pyrolysis temperature of 800 °C and atomization temperature of 1800 °C. This method allows the determination of lead with limits of detection and quantification of 0.14 and 0.47 μg L−1, respectively. The accuracy of this method for the determination of total lead was confirmed by analysing a standard reference material of trace elements in natural water supplied by NIST. Experiments using lead solutions in the presence of humic acid confirmed the efficiency of the Sep-Pak C-18 cartridge for the quantitative extraction of lead ions bound to organic complexing agents. This method was applied for the determination of labile and total lead in river water samples collected in Santo Amaro City, Bahia State, which is a region that is historically contaminated by lead as a result of a lead ore smelter that operated in the area from 1960 to 1993. For the five samples analyzed, the total lead concentrations ranged from 1.18 to 13.57 μg L−1. The fraction of labile lead ranged from 48% to 80% in four samples. The fifth sample had a labile lead content of 11%. The total carbon content was also determined in all the analyzed samples. The obtained concentrations did not present a correlation with the results obtained for lead.