Two electrochemical sensors were developed in this study, with their preparations using two nanomaterials with remarkable properties, namely, carbon nanofibers (CNF) modified with Fe3O4 nanoparticles and multilayer carbon nanotubes (MWCNT) modified with Fe3O4 nanoparticles. The modified screen-printed electrodes (SPE) were thus named SPE/Fe3O4-CNF and SPE/Fe3O4-MWCNT and were used for the simultaneous detection of heavy metals (Cd2+, Pb2+, Cu2+ and Hg2+). The sensors have been spectrometrically and electrochemically characterized. The limits of detection of the SPE/Fe3O4-CNF sensor were 0.0615 μM, 0.0154 μM, 0.0320 μM and 0.0148 μM for Cd2+, Pb2+, Cu2+ and Hg2+, respectively, and 0.2719 μM, 0.3187 μM, 1.0436 μM and 0.9076 μM in the case of the SPE/ Fe3O4-MWCNT sensor (following optimization of the working parameters). Due to the modifying material, the results showed superior performance for the SPE/Fe3O4-CNF sensor, with extended linearity ranges and detection limits in the nanomolar range, compared to those of the SPE/Fe3O4-MWCNT sensor. For the quantification of heavy metal ions Cd2+, Pb2+, Cu2+ and Hg2+ with the SPE/Fe3O4-CNF sensor from real samples, the standard addition method was used because the values obtained for the recovery tests were good. The analysis of surface water samples from the Danube River has shown that the obtained values are significantly lower than the maximum limits allowed according to the quality standards specified by the United States Environmental Protection Agency (USEPA) and those of the World Health Organization (WHO). This research provides a complementary method based on electrochemical sensors for in situ monitoring of surface water quality, representing a useful tool in environmental studies.