Hi @buraktanriverdi,
As with any active sensor, to avoid affecting the measurements you’ll need a material that is as transparent as possible to what the sensor is made to detect. In the case of sound waves that means you’ll want something with a constant density, and preferably as close as possible to the density of the fluid the sensor is in (to avoid significant acoustic reflections). The smallest density change is none at all (a.k.a. a hole / no cover), so where possible it’s best to leave gaps in the sensing direction(s) (e.g. for a scanning sonar that would be at the sides of the sensor head - the one in your image may have reduced intensity measurements in the directions of the vertical sections of the cover, depending on the material).
Note that since water pressure changes with depth and temperature, if you have a fully enclosed protective cover there will be a variable pressure differential as the vehicle moves around, unless you include a mechanism to pressurise the enclosure to the level surrounding the vehicle (e.g. passively with material flexing or a valve, or actively with some kind of pump). That effect may not be particularly significant for the pressure ranges the sensor operates in, but should perhaps be considered.
It is likely also beneficial to have a mount for your cover that is acoustically (and preferably also electrically) isolated from the sensor, to avoid adding ‘noise’ to the sensor readings (e.g. by prolonging the existing vibrations when the sonar transmits a pulse, or adding other distortions as each pulse leaves and returns).
This cover may be of interest, although it was designed more to resolve some noise issues with the vehicle it was used on than to provide external protection.