Developing metal-organic framework (MOF)-based fluorescent probes for efficient detection and discrimination of polluting ions in groundwater is vital for environmental protection and human health. In this paper, we prepared two luminescence-active transition MOFs, namely, Zn-MOF and Cd-MOF, and conducted sensing experiments. The results show that they both exhibit multiple-target detection for Fe, Pb and Cr(VI) with high sensitivity, good anti-interference ability and good recyclability even with different frameworks. In addition, Eu-incorporated samples, Eu@MOFs, with dual-emission have been fabricated efficient encapsulation of Eu ions into the MOF host. As expected, Eu@MOF hybrids also act as multi-target and self-calibrated probes to selectively detect Fe and Cr(VI) ions. However, the quenching efficiencies of the original MOFs towards Fe are higher than those of Eu@MOFs. Thus, we could differentiate Fe, Pb and Cr(VI) ions by comparing the changes of fluorescence emission between Eu@MOFs and the original MOFs. The recognition mechanism may be attributed to the competitive energy absorption between MOFs or Eu@MOFs and the analytes.