This study presents for the first time valuable results of lead (Pb) accumulation in zooplankton from a southwestern Atlantic temperate estuary, the Bahía Blanca estuary, one of the most important and industrialized coastal environments of Argentina. It considers Pb concentrations in zooplankton organisms as well as in the dissolved and particulate phases. These fractions were analyzed on account of their important role in the biogeochemical cycles of trace elements in estuarine environments. In addition, the major physicochemical variables, i.e., nutrients, and pigment concentrations, and zooplankton composition and abundance, were also considered to understand Pb levels in the above-mentioned fractions. Samplings were performed from March to December 2005 with a bimonthly frequency and comprised a study area with stations located near industrial settlements and other stations a few kilometers far from these points. The results of the physicochemical variables and nutrients and pigments agreed with historic values for the estuary and did not present any evidence of abnormalities. Dissolved Pb presented a mean concentration of 2.15 ± 0.46 μg L−1, whereas particulate Pb presented a mean concentration of 13.52 ± 3.07 μg g−1 dry weight (dw). In the mesozooplankton, represented by copepods, the mean concentration was similar to the particulate fraction (13.38 ± 4.41 μg g−1 dw), whereas in the macrozooplankton, represented by mysids, it was lower (9.81 ± 1.89 μg g−1 dw). Thus, Pb concentrations were relatively high in the dissolved and particulate phases. Moreover, zooplankton accumulated important concentrations of this metal, which was mainly incorporated through suspended particulate matter (SPM). The source of Pb in all of these fractions is related to the industry discharges as well domestic sewage located near the sampling stations. Finally, through these results, it was possible to show the importance of zooplankton and SPM in the biogeochemical cycle of Pb as well as the interaction between these fractions in an estuarine and anthropogenic environment, such as the Bahía Blanca estuary.