In the area of water injection, pulse telemetry is a new and effective communication technology which is critical for the intelligent oilfield. Under a complex environment with unknown noises, numerous problems need to be solved in the process of pulses identifying and data decoding, and there are difficulties in researching the related algorithms. In this paper, the characteristics of the pulse signals and noises are analysed respectively, and an adaptive filter algorithm is applied to reduce the impact of noises in pulse signal processing. Then a new adaptive generalized crosscorrelation algorithm is proposed to extract pulses by using a new weighted function, which can restrain interferences and noises in the frequency domain. By means of these algorithms, the pulse signal is more obvious with effective noise restraint, so these algorithms are more appropriate in water injection. Final results of field test indicate the algorithms have a high recognition performance and they meet the requirements of engineering application.