Discriminating the potential sources contributing to lacustrine sediment is helpful for decision-making for catchment soils and lake management strategies within lake-catchment systems. Using a sediment fingerprinting approach from the multivariate mixing model, the spatiotemporal sources of geology and land use were identified in a small agricultural catchment in southwest China. Results showed that sediment accumulation rates (SARs) were estimated to range from 0.002 to 0.065 g cm−2 a−1 (mean 0.015 ± 0.016 g cm−2 a−1), which has a positive correlation with instrumental Indian Summer Monsoon (ISM) precipitation. Time-integrated sources were divided into four zones in combination with the changes in SARs, which were qualitatively and quantitively interpreted by particle size, and precipitation, and historical land use polies over the past ~160 years. Spatially, Quaternary granite (QG) in geology and channel bank (CB) in land use were the dominant contributors to the lakeshore sediment, respectively. Two relatively higher contributions of abandoned land (AL) to lakeshore sediment were found during the periods of 1930s–1950s and post-1990s, which originated from the dual impacts of topographical factors of slope gradient and elevation, and socioeconomic factors of the gap of farmer’s expenditure to income. The results illustrate that restricting the farmland to be abandoned would be useful for reducing the soil erosion within the lake-catchment system.