Spatially localized methods in spectroscopy often operate with magnetic field gradients for volume selection. The eddy currents induced by these gradients produce time-dependent shifts of the resonance frequency in the selected volume, which results in a distortion of the spectrum after Fourier transformation. In whole-body systems the complete compensation of eddy currents is a difficult procedure. To avoid this, a correction method is proposed for proton spectroscopy, which uses the signal of prominent water protons as a reference for the water-suppressed signal. The correction is performed in the time domain, dividing the water-suppressed signal by the phase factor of the water signal for each data point. The corrected spectra have a good resolution as shown by phantom measurements and brain and muscle spectra of volunteers.