Biological effects measurements in fish and blue mussel are fundamental in marine environmental monitoring. Nevertheless, currently used biomarkers may be confounded by basic physiological phenomena, such as growth, reproduction, and feeding, as well as thereby associated physiological variation. Here, we present a number of supporting variables, which are essential to measure in order to obtain reliable biological effects data, facilitate their interpretation, and make valid comparisons. For fish, these variables include: body weight, body length, condition, gonad maturation status, various somatic indices, age, and growth. For blue mussels, these variables include: volume, flesh weight, shell weight, and condition. Also, grossly visible anomalies, lesions, and parasites should be recorded for both fish and blue mussels. General confounding factors and their effects are described, as well as recommendations for how to handle them.