The use of an iminodiacetic resin for trace metal preconcentration from sea-water does not allow a complete removal of the matrix, since significant amounts of alkali and alkaline earth elements are retained by the resin and co-elute with the analytes. The interfering effects due to sodium, potassium, calcium and magnesium on the electrothermal atomization of cadmium, lead, copper, iron and manganese were studied in a multivariate way. The adopted method allowed both an accurate quantification of the signal variations due to the matrix elements and a prediction of the analytical error in the determination by electrothermal atomic absorption spectrometry. In order to reduce the interfering effects, two different approaches were considered: chemical modification and matrix separation by pre-elution with ammonium acetate. A significant decrease of the interfering effects was observed for copper, lead and cadmium, after optimization of the thermal programs and proper choice of the chemical modifier. Differently, strong signal variations caused by the matrix were observed for iron and manganese, for each condition. Matrix separation by selective elution with ammonium acetate was more effective, allowing the complete suppression of matrix effects for all the considered elements. The results were confirmed by the analyses of the sea-water reference materials CASS-3 and NASS-5.