Four different sample treatment methods for the determination of trace elements have been compared: a total digestion with HNO3-H2O2-HF using microwave, and three different standardized methods of fractionation: BCR three-steps sequential extraction, USEPA standard 3050B and ISO standard 11466. The four treatment methods were applied to the determination of Cu and Ni in four samples collected in different areas of Cienfuegos Bay (Cuba). The location of samples and the analytes were selected on the basis of results obtained by previous studies. Analyses following total digestion and BCR three-steps procedure were performed by inductively coupled plasma mass spectroscopy whereas analyses following EPA and ISO procedures were performed by flame atomic absorption spectroscopy. The results obtained have been compared with an estimated anthropic fraction evaluated in each sampling point as the difference between the total concentration and an estimated background concentration level. The BCR three-steps provided the best approximation of the estimated anthropic fraction and was therefore applied also in the determination of Pb and Cd for further consideration.