At one time I use to live in Corpus Christi, Texas. Down there, like any coatal city, salt and humidity really takes its course in causing detoriation and discoloration.
The underpasses were really getting hit with salt, algea and brown coloring.
The city had an article of how they were going to stop this condition. they used liquid silicon in High PSI's power washers and sprayed the under steel and concrete. They were sealing it from the environment.
Why could you not seal your mortar? There is grout sealant for tile that is silicon. Go get it and stop this leaking.
you might have to spray quite allot to penetrate into the spaces.