Removal of organic sediment from lakes and ponds is an established management technique that is intended to enhance sport fisheries, improve boater access, and increase stormwater capacity. Data on the effects of this management technique on lake ecosystems are limited. Our objective was to determine the effect of mechanical sediment removal on herpetofauna at five sites in northern Florida. We collected a total of 883 individuals of 31 species of herpetofauna excavated by machinery during sediment removal. Across the five sites, the average number of individuals collected was 177 per site (SD = 119, range = 71–310). The most abundant herpetofauna we encountered were aquatic turtles (Trachemys scripta, Chelydra serpentina) and large aquatic salamanders (Amphiuma means, Siren spp.). Mortality from sediment removal operations may have a detrimental effect on herpetofauna populations, especially species that depend on dried lake sediments for aestivation or with limited dispersal abilities.