Reservoir sedimentation poses a significant challenge to water resource management. Improving the lifespan and productivity of reservoirs requires appropriate sediment management strategies, among which flushing operations have become more prevalent in practice. Numerical modeling offers a cost-effective approach to assessing the performance of different flushing operations. However, calibrating highly parametrized morphological models remains a complex task due to inherent uncertainties associated with sediment transport processes and model parameters. Traditional calibration methods require laborious manual adjustments and expert knowledge, hindering calibration accuracy and efficiency and becoming impractical when dealing with several uncertain parameters. A solution is to use optimization techniques that enable an objective evaluation of the model behavior by expediting the calibration procedure and reducing the issue of subjectivity. In this paper, we investigate bed level changes as a result of a flushing event in the Bodendorf reservoir in Austria by using a three-dimensional numerical model coupled with an optimization algorithm for automatic calibration. Three different sediment transport formulae (Meyer-Peter and Müller, van Rijn, and Wu) are employed and modified during the calibration, along with the roughness parameter, active layer thickness, volume fraction of sediments in bed, and the hiding-exposure parameter. The simulated bed levels compared to the measurements are assessed by several statistical metrics in different cross-sections. According to the goodness-of-fit indicators, the models using the formulae of van Rijn and Wu outperform the model calculated by the Meyer-Peter and Müller formula regarding bed patterns and the volume of flushed sediments.