A methodology to identify the partial blockages in a simple pipeline using genetic algorithms for non-harmonic flows is presented in this paper. A sinusoidal flow generated by the periodic on-and-off operation of a valve at the outlet is investigated in the time domain and it is observed that pressure variation at the valve is influenced by the opening size of blockage and its location. In this technique, the unsteady (steady oscillatory) pressure time series at only one location is required to identify two blockages. In the proposed methodology, thesolution of the governing hyperbolic PDEs of pipe flow is obtained using the method of characteristics. For any piping system similar to the hypothetical pipe system used in the simulations, generalized best amplitude and best frequency of the valve operation are determined, which give maximum deviation in pressure responses for a specific blockage at different locations for a given constant-head reservoir. The generalized best amplitude and best frequency of the valve operation are also obtained for two blockages. Accuracy of the proposed methodology in identifying blockages in a hypothetical simple pipe system with increased noise in the simulated measurements is studied. A non-dimensional variable is proposed to determine whether the proposed methodology is applicable to isolate partial blockages in a piping system. Finally, the proposed methodology is experimentally validated on a laboratory piping system for a single blockage and two blockages.