Given the great importance of the Yundang lagoon (China), a detailed evaluation and source identification of multiple potentially toxic elements (PTEs) is required. Low concentrations of the PTEs were found in the Diversion canal, while high in the Main canal, Inner lagoon, and Outer lagoon. Evaluation results indicated that the pollution of PTEs was widespread and that the extremely high eco-risks and evident toxicity were owing to the great contributions of Hg and Cd. The positive matrix factorization model demonstrated that the PTEs were from both natural and different types of anthropogenic sources. TOC played a critical role in the PTEs. It was also found that the limited environmental carrying capacity and the poor hydrological condition of the lagoon may still accumulate the pollution in a progressive fashion. These findings provide detailed information on making effective strategies of new directions for long-term prevention of PTEs pollution in the landscape urban lagoon.