Water surface photovoltaic (PV) is in the early stage of development, facing the problem of weighing economic and environmental benefits. Due to the lack of long-term statistical data and complex environmental impact, it is difficult to carry out effective benefit assessment for water surface PV projects based on existing methods. This paper, focusing on ecological environment impact instead of carbon emission, proposes the economic and environmental synergies assessment model of water surface PV projects. The core of the model is to use the gain estimation of cross-spectrum analysis to evaluate the consistent fluctuation of economic benefit and environmental benefit. In order to expose the gain spectrum, the trend component of economic benefit is extracted by singular spectrum analysis, and the biological and chemical factors of environmental benefit are identified by factor analysis. An empirical study on a 10MWp "fishery and photovoltaics integration" demonstration project in Jiangsu Province of China is conducted. The assessment result shows that the economic and environmental synergies of the project are not optimal, and the economic benefit should be reduced to mitigate the ecological damage. The empirical study shows that the assessment model is insensitive to factor weight distribution, and is not affected by noise. (C) 2019 Elsevier Ltd. All rights reserved.