Understanding the effects of land use on riparian systems is dependent upon the development of methodologies to recognize changes in sedimentation related to shifts in land use. Land use trends in southern New England consist of shifts from forested precolonial conditions, to colonial and agrarian land uses, and toward modern industrial–urban landscapes. The goals of this study were to develop a set of stratigraphic indices that reflect these land use periods and to illustrate their applications. Twenty-four riparian sites from first- and second-order watersheds were chosen for study. Soil morphological features, such as buried surface horizons (layers), were useful to identify periods of watershed instability. The presence of human artifacts and increases in heavy metal concentration above background levels, were also effective indicators of industrial–urban land use periods. Increases and peak abundance of non-arboreal weed pollen (Ambrosia) were identified as stratigraphic markers indicative of agricultural land uses. Twelve 14C dates from riparian soils indicated that the rise in non-arboreal pollen corresponds to the start of regional deforestation (AD 1749 ± 56 cal yr; mean ± 2 SD) and peak non-arboreal pollen concentration corresponds to maximum agricultural land use (AD 1820 ± 51 cal yr). These indices were applied to elucidate the impact of land use on riparian sedimentation and soil carbon (C) dynamics. This analysis indicated that the majority of sediment and soil organic carbon (SOC) stored in regional riparian soils is of postcolonial origins. Mean net sedimentation rates increased ∼100-fold during postcolonial time periods, and net SOC sequestration rates showed an approximate 200-fold increase since precolonial times. These results suggest that headwater riparian zones have acted as an effective sink for alluvial sediment and SOC associated with postcolonial land use.