In order to estimate numbers of single species freshwater fish, the passive acoustic signals of different quantities crucian carp and bream fish were used as samples. The acoustic signals of the freshwater fish were collected by the HTI-96-MIN standard hydrophone. The extracting schemes of sample characteristics were compared by using 4 ~ 6 layer wavelet packet decomposition algorithms. The short-time average zero-crossing rate and the frequency band energy calculated by 6 layer wavelet packet decomposition algorithm were determined as the signal characteristics of crucian carp. And the characteristics of bream fish were the frequency band energy calculated by 6 layer wavelet packet decomposition algorithm only. According to the research results of different sample sets dividing methods, the final sample sets dividing methods of crucian carp and bream fish were Rank-SPXY (m=10) and Rank-SPXY (m=5). Furthermore, the key characteristics of the samples were chosen by competitive adaptive reweighted sampling. Finally, some numbers estimate models of the freshwater fish were established with the multiple linear regression and partial least squares regression. The results indicated that the performance of the multiple linear regression model was better. The multiple correlation coefficients of the numbers estimate models of crucian carp and bream fish were 0.835 and 0.893, and the relative percent deviations were 1.79 and 2.01, respectively. The numbers estimate methods proposed had good performance. It provided a new means for monitoring the freshwater fish quantity.