The risk assessment of trace elements of different environmental media in conventional and organic greenhouse vegetable production systems (CGVPS and OGVPS) can reveal the influence of different farming philosophy on the trace element accumulations and their effects on human health. These provide important basic data for the environmental protection and human health. This paper presents trace element accumulation characteristics of different land uses; reveals the difference of soil trace element accumulation both with and without consideration of background levels; compares the trace element uptake by main vegetables; and assesses the trace element risks of soils, vegetables, waters and agricultural inputs, using two selected greenhouse vegetable systems in Nanjing, China as examples. Results showed that greenhouse vegetable fields contained significant accumulations of Zn in CGVPS relative to rice–wheat rotation fields, open vegetable fields, and geochemical background levels, and this was the case for organic matter in OGVPS. The comparative analysis of the soil medium in two systems with consideration of geochemical background levels and evaluation of the geo-accumulation pollution index achieved a more reasonable comparison and accurate assessment relative to the direct comparison analysis and the evaluation of the Nemerow pollution index, respectively. According to the Chinese food safety standards and the value of the target hazard quotient or hazard index, trace element contents of vegetables were safe for local residents in both systems. However, the spatial distribution of the estimated hazard index for producers still presented certain specific hotspots which may cause potential risk for human health in CGVPS. The water was mainly influenced by nitrogen, especially for CGVPS, while the potential risk of Cd and Cu pollution came from sediments in OGVPS. The main inputs for trace elements were fertilizers which were relatively safe based on relevant standards; but excess application caused trace element accumulations in the environmental media.
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