Anthropogenic contaminants are transported into estuaries during excessive rainfall events. These contaminants can impact the physiology of aquatic species, threatening fisheries sustainability, and thereby the future of global food security. Decapod crustaceans are one of the most economically important groups harvested from estuaries, and may be highly exposed to contaminants through both sediment and water. This group has received relatively little research attention and hence a quantitative evaluation of the impacts of contaminant exposure on physiology is required to better understand any impacts to fisheries. We conducted a systematic review and meta-analysis evaluating the physiological responses of harvested estuarine decapods to contaminants and flooding. A total of 140 research articles were identified and 341 effect sizes (log response ratios) were calculated. We found that exposure to various metals, pesticide chemical classes, and per- and poly-fluoroalkyl substances at environmentally relevant concentrations negatively affected key decapod physiological processes (ranging –0.73 to –0.07), including acetylcholinesterase activity, the composition of biochemical constituents, growth, metabolism, osmoregulation and oxidative stress defences. Under increasing climatic variability, harvested estuarine decapods may be increasingly exposed to contaminants, with implications for global food security and seafood consumer safety.