It is very important for dam safety control to identify reasonably dam behavior according to the prototypical observations on deformation, seepage, stress, etc. However, there are many cases in which the noise corrupts the prototypical observations, and it must be removed from the data. Considering the nonlinear and non-stationary characteristics of data series with signal intermittency, an ensemble empirical mode decomposition (EEMD)-based method is presented to remove noise from prototypical observations on dam safety. Its basic principle and implementation process are discussed. The key parameters and rules, which can adapt the noise removal requirements of prototypical observations on dam safety, are given. The displacement of one actual dam is taken as an example. The noise removal capability of EEMD-based method is assessed. It is indicated that the dam displacement feature can be reflected more clearly by removing noise from prototypical observations on dam displacement. The statistical model, which is built according to noise-removed data series, can provide the more precise forecast for structural behavior.