Despite the growing interest in recreational boating and the increasing number of marinas along the world's coastlines, environmental knowledge of these ecosystems is still very scarce. Detailed data of pollutants in marinas are necessary to provide a global approach of environmental risks in the context of international management strategies. In the present study, a set of 64 variables (30 in seawater and 34 in sediments) were measured to compare marinas from the Southern Iberian Peninsula (SIP). Uni and multivariate analyses showed significant differences among marinas, evidencing the importance of management on a local scale. The most relevant variables determining these differences were turbidity and the biocide Irgarol 1051 in seawater, and granulometry, hydrocarbons and faecal coliforms in sediment. The use of normalization techniques with Al or Fe, and the suitability of different methodologies to measure Total Organic Matter in marinas were also discussed. Additionally, we perform a comprehensive literature review of worldwide marina stressors and develop a simple and straightforward method for assessing environmental quality. The method was tested using SIP marinas and was based on the comparison of 15 selected sediment stressors with background values, concentrations of worldwide sediment quality guidelines (SQGs), and reference conditions/security thresholds established by the programme of coastal waters in port areas (ROM 5.1). A global score was assigned using a new proposed index, Marinas Environmental Pollution Index (MEPI), ranging from 0 to 150 points according to the environmental quality (<90: bad, 90–120: moderate, >120: good). MEPI of marinas from SIP ranged from 60 to 110 points indicating bad or moderate levels of pollution. Environmental quality is one of the decisive factors for awarding eco-labels or eco-certifications, such as Blue Flags in marinas. Therefore, pollution baseline information and environmental tools are mandatory for correct assignation of these awards and necessary for assessing the efficiency of management actions.