Nearly one in five reptile species is at risk of extinction. Changes in habitat area, its configuration, and vegetation diversity could affect habitat use, but their relative importance is understudied. We assessed how these factors affected reptile presence in agricultural landscapes in Iowa, USA, using 695 cover boards visited 16,441 times in 2015 – 2020. This data package contains data and R code necessary to conduct occupancy and glmm presence analyses for four snake species, one lizard species, and snakes as a functional group.