In the wild, Spotted Skiffia are found inhabiting ditches, quiet river channels, small lakes, and spring-fed ponds. The substrate is usually composed of a mixture of mud, sand, silt, and rocks. These fish typically prefer relatively shallow depths of up to 1 metre. The vegetation comprises Lemna (duckweed) spp., Typha (bulrush) spp., and water hyacinths, along with plenty of green algae. Some habitats are abundant with roots.