Zooplankton channels energy and various inorganic and organic substances from primary production to consumers at higher trophic levels; thus, its nutritional value as well as content of harmful substances may have profound effects on marine food webs. Indicators of environmental stressors such as oxidative stress biomarkers are highly useful in estimating how environmental factors affect lower levels of the food web. These biomarkers were determined in field-collected brackish water calanoid copepods Limnocalanus macrurus to analyze possible spatial variations in specimens collected from open-sea areas of the northern Baltic Sea. L. macrurus from the Bothnian Sea showed elevated levels of glutathione metabolism-associated enzyme activities and total glutathione (totGSH), whereas samples from the Gulf of Finland showed higher levels of superoxide dismutase activity (SOD) and lipid per oxidation (LPX), and a lower ratio of reduced to oxidized glutathione (GSH/GSSG). Hydrographic factors and selected indirect proxies describing general contaminant loads in the study areas partly explained the observed differences in biomarker values. The higher levels of SOD, LPX and lower GSH/GSSG together with high concentrations of polychlorinated dibenzodioxins/furans (PCDD/Fs) and polychlorinated biphenyls (PCBs) measured in the L. macrurus samples suggest the presence of multiple environmental stressors in the Gulf of Finland compared to the Bothnian Sea. The novel miniature biomarker measurement methods used and results obtained can be further applied in studies on the effects of environmental stressors in zooplankton species and communities in conjunction with environmental quality assessments.