The Yangtze-to-Huaihe Water Diversion (YHWD) project has raised concerns about balancing economic benefits and ecological impacts in Lake Caizi, a nationally protected wetland recognized by the World Wildlife Fund. To assess post-diversion contamination and ecological risks, seasonal variation in polycyclic aromatic hydrocarbons (PAHs) was investigated in surface sediments from Lake Caizi. Total PAH concentrations were 103–565 ng/g dw in the wet season, marginally exceeding the 97.1–526 ng/g dw observed in the dry season. The lowest levels occurred in the western sub-lake (Lake Xizi), showing marked declines relative to a decade ago, attributable to enhanced wastewater treatment, farmland-to-lake restoration, and a 10-year fishing ban. Conversely, PAH concentrations in the main lake, particularly the southeastern and northern sectors of the Caizi route, have increased, reflecting pollutant inflows from Zongyang County via the Yangtze River and accumulation driven by the diversion flows. The diagnostic ratio and positive matrix factorization model indicated biomass burning as the dominant PAH source in Lake Xizi across seasons. In contrast, PAH in the main lake were primarily derived from petroleum combustion and leakage, with coal combustion during the wet season shifting to coal combustion dominance in the dry season due to the seasonal halt of shipping activity. Although overall ecological risk remains low in Lake Caizi, localized hotspots near the Caizi routes and industrial zones pose moderate-to-high risks, necessitating continuous monitoring in the future.