Baltic archipelago areas have high nature values despite being polluted from various antrophogenic activities within the Baltic Sea catchment area and from long-range transport of airborne substances. The discovery of environmental problems in the Baltic Sea in the 1960s led to countermeasures that gradually gave results in reducing the toxic pollution, e.g. from PCBs. Today, much of the environmental management is focused on reducing the effects of eutrophication. There is a demand from society on science to develop strategies that can direct remedial actions so that the cost-effectiveness is maximised. This work focuses on how mass-balance models can be used to understand how coastal ecosystems are controlled by abiotic processes and to predict the response to changes in loading of different substances. Advection, sedimentation and burial are examples of general transport processes that are regulated by morphometrical characteristics, e.g. size, form, effective fetch and topographical openness. This is why different coastal areas have different sensitivity to loading of pollutants. A comparison of six phosphorus and chlorophyll models of different complexity showed that the model performance was not improved with more state variables of total phosphorus (TP) than two water and two sediment compartments. Modelling chlorophyll as a separate state variable did not improve the results for individual values compared to a simple regression against total phosphorus in surface water. Field investigations of the phosphorus content in accumulation sediments along the coast of Svealand showed a distribution pattern that probably is related to differences in the redox status. The average content of mobile phosphorus was much higher than previously found in offshore Baltic sediments indicating that sediments may play an important role for the phosphorus turnover in Baltic archipelago areas. A one-year field study to measure the levels of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in water, sediments and fish during different seasons was carried out in Kallrigafjärden Bay. The collected data set was used to test a mass-balance model for PCCD/F-turnover. It was possible to reproduce the concentrations of different PCDD/F-congeners with high accuracy using a general model approach, including one water compartment and two sediment compartments, indicating that the applied model has the necessary qualifications for successful predictions of PCDD/F-turnover in Baltic coastal areas. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 736