Somewhere in your building is a pipe that connects to open air. This is important for ensuring proper draining of the pipes when you flush/shower/use the sink. Anyway, this means outside air pressure does act on the waste water in your home. Wind is just air moving from higher pressure to lower pressure. Also velocity is inversely proportional to pressure. So when a gust of wind blows by that opening, it creates some negative pressure, which tries to suck water through your drain pipes. It doesn’t suck very hard, but enough to cause those little waves and ripples in your toilet bowl.
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