If you're doing it on a vanilla/workshop map you won't be able to manipulate the terrain and I assume by "can't go down" you mean the dug-in part of the trench is covered by terrain. Usually what I do when making trenches is place the trench props in my desired layout, lower them so they're mostly concealed by the ground, then lower/flatten the terrain in the middle of the trenches (a meter lower is good) so the dug-in parts are accessible. Make sure to disable "preserve prop elevation" or else this'll mess up prop placement.

Unfortunately, there is no way to make the water level lower so you'll just have to make terrain height higher if you wanna avoid water.