Time of arrival (ToA) estimation is essential for many types of remote sensing applications including radar, sonar, and underground exploration. The standard method for ToA estimation employs a matched filter for computing the maximum likelihood estimator (MLE) for ToA. The accuracy of the MLE decreases rapidly whenever the amount of noise in a received signal rises above a certain threshold. This well-known threshold effect is unavoidable in several important applications due to various limitations on the power and the spectrum of a narrowband source pulse. A measurement performed in the presence of the threshold effect employs a receiver which operates in the semi-coherent state. Therefore, the conventional methods assuming a coherent state receiver should be adapted to the semi-coherent case. In this paper, a biosonar-inspired method for the semi-coherent ToA estimation is described. The method abandons the exploration of an echo signal by a single matched filter in favor of the analysis by multiple phase-shifted unmatched filters. Each phase-shifted unmatched filter gives rise to a biased ToA estimator. The described method uses regression for combining these estimators into a single unbiased ToA estimator that outperform the MLE in the presence of the threshold effect.