Water pollution is a key threat for lake ecosystems in China, and estimating ecosystem services value from the perspective of water pollution is of great significance to understand and restore ecosystem functions of a lake. Since the economic loss due to water pollution is ignored in the current evaluation of ecosystem services value, a new model for estimating the ecosystem services value of a polluted lake is established by incorporating the economic losses from water pollution to improve the conventional methodology. This model was applied to Lake Dianchi to obtain its net ecosystem services value. The results showed that the average ecosystem services value of Lake Dianchi reached 38.655 billion Yuan per year during the period of 2006-2015. Water pollution has altered the structure of ecological value of Lake Dianchi. The water supply service value of the lake dropped to zero, while the atmospheric adjustment, tourism, and water storage emerged as the major contributors. The economic losses caused by water pollution amounted to 1.523 billion Yuan per year, mainly from the costs of ecological water supply and algae removal in the lake. Taking into account both ecosystem services value and economic losses in the lake, the net ecosystem services value was 37.133 billion Yuan per year, accounting for 11.7% of the total local GDP. The rationality of the evaluation results was enhanced by incorporating the water pollution losses into the evaluation of ecosystem services of lake, making this ecosystem services value estimation model more authentic than the conventional methodology to reflect the comprehensive influence of human disturbance on the lake ecosystem.