Algorithms are presented for the accurate time of arrival difference estimation of high frequency narrow band echolocation clicks from Harbor Porpoise. These clicks typically have a center frequency of around 130 kHz (wavelength ∼1.2 cm) and duration of <0.1 ms. When using hydrophones spaced centimeters apart, spatial aliasing can cause large errors on inter-hydrophone timing measurements due to the incorrect peak in the cross-correlation function of two signals being selected. It is shown that at sample rates of less than about 6 times the fundamental frequency, the incorrect correlation peak will be selected in 55% of measurements leading to large errors in time of arrival estimates. For clicks with a SNR > 10 dB these errors can be reduced by over two orders of magnitude through a combination of up-sampling the data and parabolic interpolation of peaks in the cross-correlation functions.