A detailed study of sediment components and selected metals has been carried out in two mudflat cores collected from the creeks of Kalinadi Estuary, India, in order to assess the variations in distribution of sediment components, metals, and the controlling processes, including early diagenetic movements, if any. Grain size analyses reveal the possibilities of three episodes of deposition in a highly varying depositional environment with overall fining up of the cores. Organic carbon (OC) is comparatively high in muddy Core KM, which was collected from a more sheltered creek with a narrow mouth in the estuarine interior, than sandy Core KH, which was collected from a creek with a wide mouth nearer to the sea. Geochemical data show an upper zone of marked enrichment of all trace metals, including Fe and Mn, in both the cores. The variations in sediment components as well as associated metals between the two cores reveal variations in controlling factors including the morphology setup. The distribution of trace metals in Core KH are controlled by the proportions of finer fraction of sediments, degradation of organic carbon, and redox-sensitive Fe and Mn oxides, while the distribution of trace metals in Core KM are probably controlled by the finer sediments as well as by redox-sensitive Fe and Mn oxides.