The water of the mangrove ecosystem and surrounding coastal areas are gradually shrinking due to the intense destruction. Therefore, the effects of the physicochemical properties of the habitat water on the in-habitant species must be studied. Scylla sp. is involved in the food chain and bioturbation structure formation in mangrove forests. Five major electronic databases, such as PubMed, Scopus, Web of Science, AGRICOLA, and Google Scholar, were systematically searched to review the cause and effects of influencing abiotic factors, mainly physicochemical properties of habitat water, including water pollution on Scylla sp. Responses of mud crabs at biochemical, molecular, physiological, growth, reproduction, and production level were independently reviewed or in relation to physicochemical properties of habitat water, pathogens, heavy metals, and harmful chemicals present in their habitat water. Review results suggest that these crabs are mostly under threats of overfishing, varied physicochemical properties of habitat water, pathogens, heavy metals, and chemical toxicants in water, etc. At low temperatures, the expression of calreticulin and heat shock protein-70 mRNA expression is elevated. Like melatonin, the hormone serotonin in mud crabs controls ecdysteroids and methyl farnesoate at 24 °C, 26 ppt salinity, and pH 7.2 of habitat water, facilitating their reproduction physiology. Xenobiotics in habitat water induce toxicity and oxidative stress in mud crabs. These crabs are prone to infection by white spot and rust spot diseases during the winter and spring seasons with varied water temperatures of 10–30 °C. However, elevated (65%) weight gain with higher molting at the juvenile stage can be achieved if crabs are cultured in water and kept in the dark. Their larvae grow better at 30 ± 2 °C with salinity 35 ppt and 12 hL/12 hD day length. So, monitoring habitat water quality is important for crab culture.