In this paper, we considered the real-time modeling of an underwater channel impulse response (CIR), exploiting the inherent structure and sparsity of such channels. Building on the recent development in the modeling of acoustic channels using a Kronecker structure, we approximated the CIR using a structured and sparse model, allowing for a computationally efficient sparse block-updating algorithm, which can track the time-varying CIR even in low signal-to-noise ratio (SNR) scenarios. The algorithm employs a conjugate gradient formulation, which enables a gradual refinement if the SNR is sufficiently high to allow for this. This was performed by gradually relaxing the assumed Kronecker structure, as well as the sparsity assumptions, if possible. The estimated CIR was further used to form a residual signal containing (primarily) information of the time-varying signal responses, thereby allowing for the detection of weak target signals. The proposed method was evaluated using both simulated and measured underwater signals, clearly illustrating the better performance of the proposed method.