Sedimentation processes have negative socioeconomic and environmental consequences. The Compound-Specific Stable Isotopes (CSSI) technique allows for the evaluation of sediment inputs associated with different land use changes in a study region. In the present work, this technique was used in the Alhajuela Lake sub-basin, within the Panama Canal Watershed. The role of the main soil contributors to the landscape (land uses, river, runoff, slope) relevant to the sediment load within the sub-basin of Alhajuela Lake was evaluated, and the relevant indicators in the landscape were selected in order to obtain the best representative sample. The contribution levels of three (3) representative land uses (Forest, Pasture and Sediment) in the study area were evaluated for the sediments present in sixteen (16) selected mixing points. The samples collected were subjected to the standard laboratory process to obtain the carbon chain isotopic values present in the fatty acids. The results of the determinations of the carbon chain fatty acid isotope ratios were evaluated using a Bayesian mixing model that takes into account the uncertainty present in the identified source values. According to the results obtained, the source identified as Sediment has a prominent contribution in most of the mixing points. The contributions of Forest land use are important in the mixing points located north of the study area. The contributions associated with Pasture land use are relevant in the points located in the proximity of this land use. The results suggest that landslides caused by high rainfalls events (Forest and Pasture sources) cause strong sedimentation to the north of Alhajuela Lake. At the same time, a high distribution of soils deposition is observed in the area surrounding Alhajuela Lake due to the strong presence of soils with Sediment source in these places. The results obtained are consistent with observations and measurements of the sediments accumulated in Alhajuela Lake between the years 2008 and 2012.