The escalating environmental impact of rare earth elements (REEs) in freshwater ecosystems, exemplified by Hongze Lake's increasing pollution levels from sediment-bound nutrients and REEs due to human activities, necessitates a comprehensive study. Our objectives are to unravel the spatial distribution patterns of nutrients and REEs in Hongze Lake's surface sediments and assess their combined toxicity effects on aquatic biota, aiming to fill a critical gap in understanding the ecological and toxicological risks associated with these contaminants. This study employed the diffusive gradients in thin films (DGT) technique to analyze surface sediments in China's Hongze Lake for nutrients and REEs. Significant fluctuations were observed in the concentrations of phosphate (PO 4 −P), nitrate (NO 3 −N), and ammonium (NH 4 −N), with some REEs exceeding predicted no effect concentrations (PNEC) for aquatic organisms. Correlation analysis suggested complex interrelationships among these elements, indicating potential common pollution sources. Factor analysis condensed 16 variables into 4 factors, unveiling distinct spatial distribution patterns in the lake. Additionally, a probabilistic ecotoxicological risk assessment, integrating DGT-labile concentrations and toxicity data, revealed a 1.26% probability of surface sediments in Hongze Lake inducing a combined toxic effect on aquatic biota. These findings provide specific numerical insights into pollution sources and risks within the Hongze Lake ecosystem. The results offer valuable information for current and future lake management and conservation efforts.