Bonnie's Prairie contains the only sand pond protected as a nature preserve in East-Central Illinois. The site encompasses a high-quality sand pond and wet sand prairie characteristic of the Kankakee Sand Area Section of the Grand Prairie Natural Division. The area is underlain by wind-blown sand deposits. ​

 

The sand pond is a still body of typically shallow water brimming with a wide array of wetland plants including cordgrass, fowl manna grass, small-flowered water plantain, pickerel weed, bur reed, and yellow pond lily. Two very uncommon, native species of bee that gather pollen exclusively from pickerel weed occur here. A variety of waterfowl frequent the pond. Wet sand prairie lies on an adjacent flat, low area and is strongly dominated by blue joint grass with occasional water smartweed and blue flag. On the other side of the pond, a low hill supports dry-mesic sand prairie typified by plants such as little bluestem, panic grass, hairy puccoon, goat's rue, and sand milkweed.