We conducted field surveys of amphibians and reptiles over a two-year period in 16 lagoons along the eastern coastline of South Korea, and determined the habitat characteristics correlated with the number of amphibian and reptilian species and individuals. We documented 11 amphibian species and 8 reptilian species. The dominant amphibian species was the black-spotted pond frog (Rana nigromaculata), and the dominant reptilian species was the red-eared turtle (Trachemys scripta elegans), an invasive species. Among the 14 habitat characteristics, connectivity to mountainous area significantly affected the number of amphibian and reptilian individuals. Other factors, including emerged plant cover, salinity, pH, the number of birds for amphibians and connectivity to agricultural land, lagoon perimeter length for reptiles also influenced the number of species or individuals of them. Our results demonstrate that these lagoons are home to more amphibians and reptiles than has been previously known. To effectively conserve herpetofauna in the lagoon ecosystem, lagoons as well as surrounding wetlands, grasslands, and mountainous areas should be protected.