A large number of chemicals enters the marine environment via atmospheric deposition, run-off, rivers and streams, industrial effluents and municipal wastewater. To understand how chemicals affect environmental health, monitoring and assessment approaches need to combine physical, chemical and biological effect parameters from different levels of biological organization. Embryo aberrations and reproductive success in the Baltic Sea key species Monoporeia affinis have been linked to various stressors, including chemicals, and have been applied as a bioindicator of chemical pollution since the 1970s. The current thesis aimed to improve this bioindicator by linking effects at different levels of biological organization. Understanding how effects are linked, from sub-cellular effects, to decreased organism fitness and further on to populations, will improve the ability to give early warnings and understand risks that an ecosystem faces. Paper I links point sources of chemical pollution to embryo aberrations, and shows that effects can be detected 20-30 km from point sources. Paper II demonstrates on a sub-cellular level how M. affinis´ ability to cope with hypoxia is adversely affected by chemical stress, and how it could decrease fitness. Paper III link sub-cellular effects to embryo aberrations and suggests a mechanistic link between oxidative stress and embryo aberrations. Paper III also shows that sub-cellular effects respond more distinctly compared to fecundity, survival and embryo aberrations and can thus improve the ability to detect stress at an early stage. In Paper IV, a population model was developed, which shows that populations could be severely affected if levels of embryo aberrations persist at levels commonly observed in Baltic Sea. This thesis contributes to a more holistic understanding of how chemical pollution affects M. affinis, thereby improving our ability to early detect negative effects and understand potential risks that the Baltic Sea faces.