Understanding temporal and spatial distributions of naturally occurring total organic carbon (TOC) in sediments is critical because TOC is an important feature of surface water quality. This study investigated temporal and spatial distributions of sediment TOC and its relationships to sediment contaminants in the Cedar and Ortega Rivers, Florida, USA, using three-dimensional kriging analysis and field measurement. Analysis of field data showed that large temporal changes in sediment TOC concentrations occurred in the rivers, which reflected changes in the characteristics and magnitude of inputs into the rivers during approximately the last 100 yr. The average concentration of TOC in sediments from the Cedar and Ortega Rivers was 12.7% with a maximum of 22.6% and a minimum of 2.3%. In general, more TOC accumulated at the upper 1.0 m of the sediment in the southern part of the Ortega River although the TOC sedimentation varied with locations and depths. In contrast, high concentrations of sediment contaminants, that is, total polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), were found in sediments from the Cedar River. There was no correlation between TOC and PAHs or PCBs in these river sediments. This finding is in contradiction to some other studies which reported that the sorption of hydrocarbons is highly related to the organic matter content of sediments. This discrepancy occurred because of the differences in TOC and hydrocarbon source input locations. It was found that more TOC loaded into the southern part of the Ortega River, while almost all of the hydrocarbons entered into the Cedar River. This study suggested that the locations of their input sources as well as the land use patterns should also be considered when relating hydrocarbons to sediment TOC.