Understanding how environmental factors affect the reproductive success of sentinel species is crucial for ecosystem-based management. The deposit-feeding amphipod Monoporeia affinis plays a key role in the Baltic Sea. Environmental contaminants in sediments can impact embryo development in Monoporeia, and assessing embryo aberrations helps monitor contamination levels and evaluate the environmental condition of the Baltic Sea. However, non-chemical stressors like food scarcity and bottom hypoxia can also influence the reproductive performance of these amphipods. Consequently, determining chemical pollution as a significant driver of reproductive health in wild populations across different basins facing multiple stressors is challenging.Here, we used PLS-SEM to analyze the links between reproductive health, sediment contaminants, environmental variability, genetic diversity, and nutrition in M. affinis. Our study encompassed data from 30 monitoring stations in the Western Gotland Basin and the Bothnian Sea. We found that amphipod reproductive health, assayed by embryo aberration frequencies, and resource utilisation, assayed by isotopic niche metrics, were directly impacted by chemical contaminants (metals and PAHs) and non-chemical factors (temperature). Additionally, the trophic niche played a significant mediating role in embryo aberration frequency. Furthermore, temperature moderated the relationship between chemical exposure and reproduction. However, we did not find any consistent variable representing genetic diversity using commonly applied metrics in population genetic analysis and mtDNA. Consequently, the contribution of genetics to reproductive health and trophic niche remains uncertain.Our PLS-SEM analysis reveals the significant impact of environmental contaminants on reproductive outcomes. Moreover, the connection between exposure and reproductive health is stronger in the Bothnian Sea compared to the Western Gotland Basin. These findings highlight the varying challenges faced by amphipod populations in these subbasins, emphasising the need to consider these differences in the overall environmental assessment. These results establish important relationships between pressure and indicators for sentinel species, supporting the effective and science-based use of biological effect indicators in the Baltic Sea.