In a changing environment it is critical to understand how populations respond to altered habitats if we are to understand anthropogenic impacts on ecosystems and recommend adequate management strategies. Amphipods are sensitive to contaminant exposure and are useful sentinels of environmental disturbances. Monoporeia affinis is included as a sentinel in the Swedish national monitoring program to monitor benthic community ecology and biological effects of contaminants. Lethal embryo aberrations increase in M. affinis as a respond to chemical pollutants, which makes them useful as pollution-specific biological effect indicators with high ecological relevance. In this project we link monitoring data on lethal embryo aberrations from the last 20 years to other monitoring data such as phytoplankton bloom intensity and oxygen conditions. Preserved animal samples have also been analysed for stable isotopes (which can be used to describe diet and habitat use for animals) and population genetic diversity. Embryo aberrations as biological effect indicator has the potential to meet the challenges of the EU Marine Strategy Framework Directive, whereby Member States are required to develop tools for defining qualitative descriptors of Good Environmental Status, such as “concentrations of contaminants are at levels not giving rise to pollution effects” (Descriptor 8).