Chemical pollution affects the health of marine biota, key functions of the ecosystem, and endangers its biodiversity. The current environmental monitoring and assessment approach is based on chemical and ecological measurements, while the linkage between them, biological effects at the individual level, has been largely neglected. It is currently well acknowledged that the monitoring of chemical concentrations alone is not sufficient to protect populations; it considers only a tiny number of substances, while myriad others are left unnoticed. In addition, the hazards related to contaminant mixtures remain undetected. Biological effects of contaminants can be detected and measured at different levels of biological organization, i.e., from the molecular/biochemical level up to changes in populations and communities. In Baltic Sea monitoring programs, the few observations on the effects of contaminants have, for decades, mostly been made at only the higher biological organization levels, applying reproduction success parameters in top predators such as raptor birds and seals as indicators. However, recording early warning signals of contaminant exposure and effects on the health of individuals at lower biological levels makes it possible to anticipate and prevent damage at the higher levels. Moreover, it is also crucial to monitor effects at lower levels of the marine food web. The so-called biomarkers focus on changes in various biological functions and include parameters related to the detoxification of xenobiotics, oxidative stress, neurotoxicity, geno- and cytotoxicity and reproductive disorders, among others. Research on biomarkers aiming at improving their use in monitoring and assessing the contamination status of marine areas has been intensive during recent decades, although the implementation of the methods to monitoring programmes has been slow. Here, the current state of biological effects monitoring using biomarkers, as well as selected case studies in the Baltic Sea, are presented, followed by recommendations on their application in this sea area.