Elemental and isotopic compositions of organic matter in surficial sediments from five transects across Lagoa do Caçó (Brazil) were analyzed to identify the depth-related processes that affect the production and deposition of sedimentary organic matter in this shallow tropical lake. Each of four transverse transects began at a margin dominated by aquatic macrophytes (Eleocharis), crossed the central deep part of the lake, and terminated in the opposite, macrophyte-dominated margin. In each transect, TOC concentrations, C/N ratios, and δ13C values decreased between 0 and 4 m, whereas δ15N values increased. The variables remained stable in sediment from 4 m water depth to the center of the lake at 10 m. The depth-related patterns reflect differences in both the delivery and the deposition of organic matter in the lake. Organic matter is produced in abundance in the marginal area by emersed and submerged macrophyte vegetation that diminishes with depth and disappears at 4 meters. After the disappearance of macrophytes, organic matter is produced at low rates principally by open-lake phytoplankton. Drawdown of dissolved oxygen is high in the lake margins, but it is low in the oligotrophic open waters of the lake. Preservation of organic matter is consequently better in sediments of the lake margins than in deep waters. The depth-related pattern of organic matter delivery and deposition in the sediments of Lagoa do Caçó, in which water levels are sensitive to groundwater fluctuations, shows that the elemental and isotopic compositions of sediment organic matter can provide a record of changes in the paleohydrology of this and other similar shallow lake systems. © 2011 Springer Science+Business Media B.V.