Soil surface covers are critical to understanding the influence of aboveground inputs on underlying soils. Surface covers are often composed of organic material, but mountain soil surfaces are sometimes covered with rock fragments. This study compared mountain soils at two study sites in Klamath National Forest to determine the influence of surface rock fragments on physical soil properties and organic matter accumulation. One soil had a distinct surface rock fragment layer of cobbles and stones above the soil, and the other had only a layer of organic litter. Soil temperature and moisture were measured continuously for a year. Organic litter, soil organic carbon, and pyrogenic carbon were measured and described to detect differences in decomposition and microbial activity. Morphology of the surface horizons was distinctly different, and accumulation of litter around rock fragments was not continuous across the surface. The O horizons from each site show dissimilarity in decomposition, but soil organic carbon was generally similar within the mineral soils. Results indicate that surface rock fragments increased soil and near-surface temperatures, and controlled moisture movement and retention to a lesser extent. These factors may negatively influence microbial and fungal activity, which are dependent on temperature and moisture status in the litter layers around rock fragments. Examination of pyrogenic char samples suggests that surface rock fragments can control or impede the contact between aboveground inputs and underlying mineral soils. In addition, contact with soil microbes that may use char as habitat, can be prevented.