The analysis of environmental risk in historical cities facilitates the development of conservation strategies that can minimize the deterioration of historical heritage sites. Risk maps built with GIS software provide information about the probability of the main hazards in a region, and is a very useful tool to identify, evaluate and prioritize the restoration budget of a city in order to manage preventive conservation. In this paper, new methodologies are applied based on the vulnerability matrix and its relationship with static and structural factors, climate conditions, air quality and social agents. This technique has some obvious advantages in the application of risk analysis for cultural heritage conservation, such as the capability of simultaneous risk assessment and geographical references. The vulnerability study implies an on-site diagnosis analysis and requires an adapted protocol for archaeological heritage. The validation of this methodology was carried out in the historical town of Merida (Spain) with a GIS application (ArcGIS software), where the main monuments of this UNESCO World Heritage site were studied.