Quantum turbo codes (QTC) have shown excellent error correction capabilities in the setting of quantum communication, achieving a performance less than 1 dB away from their corresponding hashing bounds. Decoding for QTCs typically assumes that perfect knowledge about the channel is available at the decoder. However, in realistic systems, such information must be estimated, and thus, there exists a mismatch between the true channel information and the estimated one. In this article, we first heuristically study the sensitivity of QTCs to such mismatch. Then, existing estimation protocols for the depolarizing channel are presented and applied in an off-line manner to provide bounds on how the use of off-line estimation techniques affects the error correction capabilities of QTCs. Finally, we present an on-line estimation method for the depolarizing probability, which, different from off-line estimation techniques, neither requires extra qubits, nor increases the latency. The application of the proposed method results in a performance similar to that obtained with QTCs using perfect channel information, while requiring less stringent conditions on the variability of the channel than off-line estimation techniques.