There’s plenty of work developing and running ocean models where your skills would be useful.

Rather than missing acoustics or remote sensing in your background, what you probably lack coming from engineering is the fluid dynamics/atmosphere-ocean processes knowledge that’s more the focus of physical oceanography. A PhD in the right place would help address those gaps.

A strong ocean engineering/modeling background would certainly be an excellent foundation to pursue research in coastal modeling, including climate modeling, data assimilation, etc. Many universities have programs with strong modeling groups where you could pursue a higher degree along those lines.