Although Piezo-Electric Transducers (PZT) hydrophones are widely accepted and technologically mature in the field of Acoustic Emissions (AE) strain sensing underwater, optical fiber-based sensors are gaining more attraction due to their multiplexing capability, small size, high resolution, high sensitivity and immunity to Electromagnetic Interference (EMI). In this paper, we propose a hybrid Fiber Bragg Grating (FBG) system based on combining two apodized FBGs (AFBGs); named Nuttall and Cos8, separated by a pi-phase shift to apply it for underwater strain sensing. This combination results in optimum performance in terms of the reflection properties including high peak reflectivity, narrow Full Width at Half Maximum (FWHM), remarkable side lobes suppression, high roll-off rate, good Ripple Factor (RF) and high Detection Accuracy (DA) as well. In addition, an excellent multiplexing capability, high temperature and strain sensitivities and a stable operation over increased temperatures, strain and pressure levels (up to 250 °C, 1000 µstrain and 100 MPa) are achieved. Moreover, mechanical analysis and comparisons revealed that the Polymer Optical Fiber (POF) recorded the highest sensitivity among other fiber types and their coatings with a value of 1.43 pm/µstrain, making it applicable in the strain sensing in underwater acoustics. Furthermore, in this work, a detailed comparative study is performed between several types of interrogators targeting an optimum interrogator for the strain sensing application in underwater acoustics. The obtained results reveal that the linear edge absorption filter detection method achieves better results among the other types. But, unfortunately, when talking about the multiplexing capability, it shows a remarkable failure. Whereas, the Mach–Zehnder. Interferometry (MZI) comes in the second place with higher resolution range (103–104) with tunable sensitivity, fast measurement speed, good long-term stability, high multiplexing capability and medium cost. Accordingly, it could be applicable in the application understudy.