Understanding how different pools of sediment organic carbon (OC) are associated with trace metals is essential for interpreting biogeochemical processes in small freshwater ecosystems. This study examines spatial and interannual patterns of total organic carbon (TOC), water-extractable organic carbon (WEOC), and cadmium (Cd) in sediments collected from streams, natural ponds, and drying ditches across three contrasting regions of Lithuania during 2022–2024. TOC and WEOC exhibited pronounced spatial gradients and a marked increase in 2023, while Cd showed a similar but more moderate temporal response. Correlation analysis, principal component analysis, regression modelling, and structural equation modelling consistently indicated that WEOC is more strongly associated with sediment Cd concentrations than bulk TOC. The results suggest that TOC influences Cd distribution primarily indirectly, through its control on the water-extractable OC pool. Multivariate analyses revealed a dominant organic–metal association gradient shared by TOC, WEOC, and Cd, as well as a secondary axis reflecting partial geochemical independence of Cd. These findings highlight the functional relevance of WEOC as an interface between sediment organic matter and Cd accumulation in small freshwater systems. Incorporating WEOC into sediment monitoring may improve interpretation of trace-metal patterns under conditions of hydrological variability.