Extend Clean Out Pipe and Fill Hole with Cement
Water is very sneaky. It will always find the path of least resistance. To fix this problem you need to first find the actual source. You may have exterior sewage draining back into your house. A licensed plumber can use a dye in different areas and that dye will show up in your clean out pipe. If it does then you know where it came from and where to begin fixing the problem. If it does not, then you know that it is simply water from outside. Remember, that pipe was put there for a reason. Sealing it may cause more problems in the long run.