Environmental specimen banks (ESBs) are not a new phenomenon, but in the last decades, the steep rate in the establishment of new ESBs is a sign to address new research approaches for scientists. In this way, environmental biobanking is becoming a well-organized and effective vehicle to collect samples of high quality making them available for future researchers. The endpoints promoted in the ESBs are mainly based on chemical approaches, but the necessity to add biological endpoint is fundamental (e.g., assessment of the environmental health status). Moreover, advances and development of high sensitive, high-throughput techniques along with ecotoxicological approaches based on biomarkers are stimulating a new demand for stored specimens and associated data. Like in chemically targeted environmental specimen banking, the banked samples for the assessment of biological effects also require guidance informed by knowledge of their practices and challenges, along with policies for the correct advancement of research goals and appropriate and effective biobank governance.