The growing availability of spatial data sets and the increasing number of users from non-spatial disciplines highlight the importance of evaluating the fitness for use of such data sets in environmental and ecological applications. This article proposes and illustrates a practical methodological framework to evaluate the fitness for use of spatial data sets for environmental and ecological applications, focusing on user requirements for specified application contexts. The methodology is based on the use of metadata to analyse similarity between the data characteristics and the user’s needs or expectations for several quality indicators, and introduces the concept of ‘critical factors’, allowing users to define which quality indicators have greater importance. Examples of the evaluation are presented within the BIO_SOS (‘Biodiversity Multi-SOurce Monitoring System: From Space To Species’; FP7) project, focusing on the assessment of three different applications and respective spatial data sets. The proposed methodology encourages the implementation of spatial data quality evaluation routines in ecological assessment and monitoring programs, promoting more adequate use of geospatial data and ultimately contributing to well-supported policy and management decisions.