You have a couple of options really, you can just stir up the gravel substrate to remove the air pockets and this won't disturb the shrimp too much or if you wish to remove the brown algae your best plan of attack would be to literally move he gravel back wards and get a scraper and just go at it then pull the gravel back down into the gap between the glass and the pile of gravel again.
Don't worry about disturbing the shrimp because they will settle down again. Plan it out to reduce the amount of time you are moving and cleaning! If it helps I've got to move house soon and moving a whole tank will disturb them a hell of a lot but I'm not worried.
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