A functionalized carbon nanotubes paste electrode modified with cross-linked chitosan for the determination of trace amounts of cadmium(II) and mercury(II) by linear anodic stripping voltammetry is described. Under optimal experimental conditions, the peak current was linear in the Cd(II) concentration range from 5.9×10−8 to 1.5×10−6 molL−1 with a detection limit of 9.8×10−9 molL−1 and, for Hg(II) from 6.7×10−9 to 8.3×10−8 molL−1with a detection limit of 2.4×10−9 molL−1. The proposed method was successfully applied for the determination of Hg(II) in natural and industrial wastewater samples, and Cd(II) in sediments, human urine, natural, and industrial wastewater samples.