Pesticides can migrate and accumulate across environmental compartments, necessitating multi-medium risk assessments to ensure sustainable development and safeguard human health. Although soils and sediments are recognized as ultimate sinks for pesticides, differences in their distribution patterns and associated ecological risks remain poorly understood, posing challenges for targeted pesticide management. In this study, we analyzed the temporal and spatial distribution of 39 various historically-used and currently-used pesticides in both farmland soils and their nearby river sediments collected from the Lake Taihu Ecological Conservation Area (TECA), China. A total of 9 and 7 types of pesticides were found in soils and sediments, respectively, which were dominated by p,p'-DDE (in average of 27.7 and 4.3 ng/g), buprofezin (in average of 96.3 and 7.1 ng/g), and bifenthrin (in average of 27.6 and 6.8 ng/g). Notably, o,p'-DDT, cypermethrin, deltamethrin, and fenvalerate were exclusively detected in soil samples, whereas permethrin and prometryn were uniquely present in some sediment samples. Principal component analysis (PCA) revealed that seasonal patterns in pesticide distribution occurred only in soil samples, with no corresponding patterns observed in sediments. The risk quotient (RQ) assessment indicated the potential ecological risks posed by the detected pesticides. Although most pesticide residues detected in soils and sediments posed low ecological risks (RQ < 1), pyrethroids (especially bifenthrin in sediments) exhibited notably highly risk quotients, indicating their comparatively high ecological risks and warranting attention for management. © The Author(s), under exclusive licence to Springer Nature Switzerland AG 2025.