A sensitive mass spectrometric analysis method based on the microwave plasma technique is developed for the fast detection of trace rare earth elements (REEs) in aqueous solution. The plasma was produced from a microwave plasma torch (MPT) under atmospheric pressure and was used as ambient ion source of a linear ion trap mass spectrometer (LTQ). Water samples were directly pneumatically nebulized to flow into the plasma through the central tube of MPT. For some REEs, the generated composite ions were detected in both positive and negative ion modes and further characterized in tandem mass spectrometry. Under the optimized conditions, the limit of detection (LOD) was at the level 0.1 ng/mL using MS2 procedure in negative mode. A single REE analysis can be completed within 2~3 minutes with the relative standard deviation ranging between 2.4% and 21.2% (six repeated measurements) for the 5 experimental runs. Moreover, the recovery rates of these REEs are between the range of 97.6%–122.1%. Two real samples have also been analyzed, including well and orange juice. These experimental data demonstrated that this method is a useful tool for the field analysis of REEs in water and can be used as an alternative supplement of ICP-MS.