Methods and systems for obtaining improved joint channel estimates for a multi-user, frequency-multiplexed data transmission such as SC-FDMA or OFDM begins by estimating separate contributions of users (and/or other signal sources) to the received signal based on joint frequency domain channel estimates. A reduced data set is obtained by subtracting contributions of one or more users from the received data, leaving only the estimated contributions of the remaining users, with noise and residual estimation error signal. Time domain joint channel estimation is then performed on the reduced data set, which is feasible because the number of users has been reduced. In exemplary embodiments, the reduced data set includes only one estimated user contribution. This process is repeated to obtain channel estimates for all of the users. The method can be repeated by using the channel estimates to re-estimate the user contributions and calculate revised channel estimates.