Worldwide legislation emphasizes the need to monitor the health of aquatic ecosystems based on the response of biological quality elements to environmental conditions. A plethora of methodologies have been suggested in this sense. Lately, substantial efforts have led to the exploration of new biological quality elements from the meiobenthic compartment and the implementation of new methodologies based on environmental DNA. Due to their short life-cycles, meiofaunal organisms respond quickly to environmental variability. Changes in population dynamics and species composition are indicative of changes in environmental conditions. Recent pioneer studies have shown that biotic indices based on benthic foraminifera and nematodes can efficiently assess the health of transitional and marine ecosystems. The use of environmental DNA, as well as other fingerprinting techniques, is increasing in biomonitoring studies, and further calibrations are still needed to implement this method. The published papers in this Special Issue represent well the wide applicability of meiobenthic groups, i.e., benthic foraminifera and nematodes, allowing us to address a key ecological knowledge gap in order to convince decision makers and stakeholders about the advantage of introducing new biological quality elements in environmental biomonitoring.