The Swedish Geological Survey (SGU) and FOI have jointly conducted an environmental impact investigation at the Muskö Naval Base regarding contaminated sites, remediation and the economical consequences of such actions. The investigation was performed within a comprehensive environmental project aiming at assessing the nee for remediation plans when it comes to contaminated sites (soil, groundwater, surface water and sediment), should the enterprise be discontinued. The risk assessment was performed in accordance with the Swedish EPA Method MIFO and consisted of two phases. In a previous Phase 1, two objects were identified as requiring further investigation, namely the Fire Rescue Services training site and the rock landfill site. The present investigation consists of a Phase 2 study of the above-mentioned objects. The risk assessment was based on the results from the soil and ground water analysis. The Fire Rescue Services training site showed fairly high levels of PCBs and very high levels of organotin compounds in the groundwater. Therefore it was classified as Risk Level 2. The rock landfill site was classified as Risk Level 3, provided that a control programme is elaborated enabling the study of any possible changes beyond the proper time. The outflow of organotin compounds to the bay is likely to be low in comparison to the contribution of organotin compounds from the other activites at the naval base.