Understanding inflow dynamics in a dam lake forms the basis for optimal dam operation and management practices. However, methods pertaining to adequately determining negative inflows and addressing them, as well as quantifying uncertainties in dam inflow, have been scarcely investigated. In this study, the inflow was observed using two pairs of fluvial acoustic tomography (FAT) systems placed diagonally in a dam lake, forming a crossed-shaped pattern. The “travel-time” principle is the primary approach for measuring the inflow by FAT. The novelty of this study is in discussing the inflow characteristics within a slow water-flow environment monitored by FAT. Based on the reciprocal sound transmission, we upgraded an equation to estimate the flow direction; this newly proposed generalized equation can be used in a fluctuating flow environment. We also discussed the sound propagation characteristics for slow flow velocities. Finally, we demonstrated that a small inaccuracy in the acoustic signal, even by a sub-millisecond, can cause significant errors in measurements. One of the novel findings of this study is the detection of internal waves using the improved flow direction equation and acoustic travel-time records. Overall, this study presents a promising approach for inflow measurements under extremely slow flow conditions.