Invertebrates exist in the aquatic ecosystem and serve as intermediate consumers in the food chain, which play important roles in environmental health and as indicators of pollutant toxicity. Therefore, the sampling of organisms from marine systems will be of great importance for environmental health monitoring and ecotoxicological tests. The research targets determine sampling of marine invertebrates, both connecting with the diversity and richness of species and relating to the subsequent detection methods and toxicological technology. Thus, this chapter primarily summarized the species of marine invertebrates that were previously collected from the natural sites and laboratory experiments and the detailed methods of sampling from water systems with various research aims. Moreover, the common indexes of marine organisms, especially invertebrates, along with the environmental parameters, including water quality, are sorted out as the necessarily recorded information when sampling. This review also included comparing sampling methods of invertebrate animals in different marine ecosystems, as well as the subsequent treatment and detections of the collected specimens, which can provide the fundamental guidelines for practical application in the investigation of the marine environment. Additionally, the problems and challenges in the modern and future are discussed, including whether they can be solved with the developed sampling and detection technology aspects.