Farmers must consider real-world problems and variability to maximize yields and minimize environmental impacts when using cover crops in corn (Zea mays L.)-based cropping systems. Much of the variability encountered by farmers of the Midwest Corn Belt is due to the topographical diversity of the undulating landscape. The objectives of this study are to explore the effects of cover crops on soil organic carbon (C), both total organic C and its labile form, particulate organic C (POC), and on water retention at contrasting topographies (summit, slope, and depression). A cereal rye (Secale cereal L.) cover crop was established in the fall of 2011 at two experimental sites. At each site, the experimental design was a split-split plot with whole plot factor, topographical position, in a randomized complete block design with two replications. Topographical position affected all studied plant and soil characteristics, including aboveground plant biomass, rye residue decomposition, POC, total soil C, and soil water retention. Across all topographical positions, rye residue decomposition was similar to 5% greater in the treatment with than without cover crop. In slopes and summits, the POC in the treatment with cover crop was significantly (similar to 0.7 mg g(-1) soil [similar to 700 ppm]) greater than in the treatment without the cover crop; however, the difference was not statistically significant in depressions. The cover crop effect on both total organic C and soil water retention levels was not statistically significant. The study points to potential interactions between topography and C sequestration benefits of cover crops; however, longer experimental times are needed to detect significant differences in soil total C and water retention measurements.