In the modern Arctic the economic activity is mainly concentrated in coastal zone. This fact leads to an increase in vulnerability of nature-use activities due to natural and technogenic threats. The paper develops a scientific basis for the analysis of nature-use risks and their impacts on the coastal eco-socio-economic systems of the Russian Arctic zone. Such methodology is based on a combination of quantitative and qualitative indicators methods and matrix approaches. The risk is defined as a process structured in the form of a chain of three interrelated components: risk-source, risk-factor and risk-object, each of which has a set of classification features. This made it possible to form matrices of the components of the risk process: the risk-factor – risk-source matrix and the risk-object – risk-factor matrix. So, a risk model of Arctic nature-use processes in the Russian Arctic coastal zone has been developed. This model was tested on the example of 17 local coastal local municipalities of the Murmansk region. The use of this methodology and model as a tool for assessing and preparing measures to reduce the risks of Arctic coastal nature-use activities will contribute to increasing the effectiveness of territorial planning processes and the sustainability of Arctic coastal eco-socio-economic systems as a single complex, considering medium- and long-term environmental and socio-economic changes.