The Lake Mendota Microbial Observatory collects routine water clarity measurements alongside their microbial samples. This dataset includes measurements of water clarity collected at the central Deep Hole, collocated with a weather buoy (43°05'58.2"N 89°24'16.2"W). All measurements were collected with handheld Secchi discs. When multiple personnel performed the Secchi disc measurements, the average and standard deviation are reported. To take the Secchi depth, sunglasses are removed and the disc is lowered on the shaded side of the boat. The Secchi depth is the average between where the Secchi disc disappears while lowering it and where it reappears while raising it. Routine microbial observatory sampling continues into the present.