What are the outputs you would like to create? e.g. a Digital Surface Model (DSM), an Orthomosaic, 3D textured mesh,…
For example, if the main output is the DSM, you could add a surface in these areas and check “Use for DSM and Triangle Mesh”, similarly to what is done here: https://support.pix4d.com/hc/en-us/articles/202560449
The problem with these water surfaces, is that there are no calibrated cameras over it, so the software will not be able to project the content of the images on these areas to create an orthomosaic, i.e. there will probably be a hole in the orthomosaic in these areas.
As for areas that contain water, something that can help is to increase the overlap during the image acquisition. More about that here: https://support.pix4d.com/hc/en-us/articles/202558999 and https://support.pix4d.com/hc/en-us/articles/202557459#label5
If you just want to remove the points, the point cloud editing tool should help: https://support.pix4d.com/hc/en-us/articles/202560499
Let us know how it went