Erhai Lake, a vital drinking water source for Dali, a highland agricultural city, faces potential contamination from pesticide residues, yet limited studies have assessed their distribution and impacts. This study investigates the occurrence, transport, partitioning, and ecological risks of pesticides in the lake's dissolved phase (DP), suspended particulate matter (SPM), and sediment (SD) samples collected from 22 sites across different seasons. The results showed significant temporal variations across different media, with spatial variations driven by crop-related patterns. Atrazine, etridiazole, and cis-permethrin were identified as the most abundant pesticides in DP, SPM, and SD, respectively. Notably, the source-sink dynamics were not only driven by deposition and resuspension but influenced by multiple sources and hydrodynamic processes such as precipitation, phytoplankton biomass, organic carbon, and winds. Ecotoxicological assessments indicated that permethrin, endrin, and endosulfan sulfate posed significant ecological risks to aquatic organisms. Although human health risks from pesticides were low, ongoing monitoring of atrazine is recommended due to its extensive use around Dali City.