Design of acoustic modem becomes increasingly important in underwater sensor networks' development. This paper presents the design of a reconfigurable acoustic modem, by defining modulation and demodulation as reconfigurable modules, the proposed modem changes its modulation scheme and data rate to provide reliable and energy efficient communication. The digital system, responsible for signal processing and control, is implemented on Xilinx Virtex5 FPGA. Hardware and software co-verification shows that the modem works correctly and can self-configure to BFSK and BPSK mode. Partial reconfiguration design method improves flexibility of algorithm design, and slice, LUT, register, DSP, RAMB are saved by 17%, 25%, 22%, 25%, 25% respectively.