Macroinvertebrates metrics are reliable indicators to assess the environmental quality and ecological health. In water systems, estuarine areas are sinks and sources of nutrients and pollutants, and strongly influenced by anthropogenic activities and emission from inland. Benthic macroinvertebrates and zooplankton living in estuary and coastal are not very active organisms hence heavily impacted by surrounding environmental conditions. In this study, we assessed the water quality at the tropical coastal of Can Gio located in Southern Vietnam, based on the aquatic invertebrates and environmental variables. The organisms were monitored at 20 sampling sites along the Can Gio coastal in November 2021, April, June and August 2022. Totally, 45 invertebrate species were recorded in the Can Gio coastal. The zooplankton and benthic macroinvertebrate abundance, respectively, varied between 900 to 13,000 individuals/m3, and ranged from 30 to 120 individuals/m2. The copepods and polychaetes were dominant in both species number and abundance of the zooplankton and benthic macroinvertebrates, respectively. The water quality at the Can Gio coastal during the monitored period was from low pollution to high-moderate pollution based on the invertebrate structure, abundance and indices. The results also showed the correlation between environmental variables (e.g., turbidity and dissolved oxygen) and species richness and abundance of aquatic invertebrates. Our study revealed the important and valuable application of aquatic invertebrates for the environmental quality monitoring to protect the border of the most mangrove biosphere reserve in Vietnam.