Xがする is a phrasal verb and is most often used in phrases such as 音がする and 匂い{におい}がする and even 気がする. It is used with words that are about perceiving or sensing something. (More phrasal verbs here.)
Yet it does not really require the actual sensing part from the part of the speaker, but instead is a pretty objective way of saying that 'there is a smell' or '[something] is making a sound'. The focus is less on the sensing but rather just the existence of the sensory input.
波の音を聞く sounds odd to me. It means something like [I] listen to the sound of waves. It should be 波の音が聞こえる I hear the sound of waves.
With the 聞く verb, it would work as a request such as 波の音を聞いてみて Try listening to the sound of waves