For acoustic procedures which rely on the speed of sound to derive process parameters, the determination of the acoustic time of flight is essential. In this work, a method for the determination of the time of flight (TOF) is presented. It is intended for reverberant and noisy environments and can be applied in the gas holdup determination in bubbly liquids via acoustic transmission tomography (GHATT) for example. The method includes the selection and design of the transmitted signal to optimize the disambiguate of the autocorrelation, the narrowing of the time window based on the Fractional Fourier Transform (FrFT) to accelerate the TOF estimation. Furthermore, it includes the consideration of the system-induced signal distortion through prior quasi-anechoic measurements and the sparse reconstruction of the spatial impulse response for TOF estimation using non-negative sparse deconvolution algorithms. The method is tested analytically on numerically generated signals and various sparse deconvolution algorithms are investigated with respect to their applicability and limitations.