Multiecho sequences provide an efficient means to acquire multiple echoes in a single repetition, which has found applications in spectroscopy, relaxometry, and water-fat separation. By replacing the fly-back gradients in unipolar multiecho sequences with alternating readout gradients, bipolar multiecho sequences greatly reduce both echo-spacing and repetition interval. This offers many attractive advantages, such as shorter scan times, higher SNR efficiency, more robust field map estimation, reduced motion-induced artifacts, and less sensitivity to short T(2)*. However, the alternating readout gradients cause several technical problems, including delay effects and image misregistrations, which prevent direct application of existing water-fat separation methods. This work presents solutions to address these problems, including a post-processing method that shifts k-space data to correct k-space echo misalignment, an image warping method that utilizes a low-resolution field map to remove field-inhomogeneity-induced misregistration, and a k-space water-fat separation method that eliminates chemical-shift-induced artifacts in separated water and fat images. In addition, a noise amplification factor, which characterizes the noise present in separated images, is proposed to serve as a useful guideline for choosing imaging parameters or regularization parameters in the case of ill-conditioned separation. The proposed methods are validated both in phantoms and in vivo to enable reliable and SNR efficient water-fat separation with bipolar multiecho sequences.