As well known, silver nanoparticles (AgNPs) are being increasingly used in many different sectors due to their particular biocidal characteristics. The existence of these substances in many day life products leads to the presence of AgNPs in different environmental compartments. In particular, the aquatic ecosystem is one of the reservoirs that receive more silver nanoparticles. The affectation of different living organisms by AgNPs has been proved through several studies. Therefore, in this paper a methodology to assess the risk of AgNP for the aquatic ecosystems is presented. The methodology is based on the fuzzy logic theory, which is a proved method to deal with variables that have associated uncertainty. This is the case of many of the variables related to the AgNPs. A selection of input and output variables has been carried out after a deep research. Once the variables are identified, the fuzzy inference systems can be established. From inputs such as the size, the shape and the coating of the AgNPs, it is possible to determine the toxicity. This variable together with the media concentration will provide the final assessment of risk. To prove this methodology, a case study based on an accident has been presented. The results show how the risk of AgNPs vary with the pollutant front advance, arriving to a high risk situation. This tool can be adapted to different situations and types of nanoparticles, making a very appropriate for the decision makers.