Human activities in coastal catchments can cause the accumulation of pollutants in seafood. We quantified the concentration of heavy metals, pesticides and PFASs in the flesh of the fisheries species yellowfin bream Acanthopagrus australis (n = 57) and mud crab Scylla serrata (n = 65) from 13 estuaries in southeast Queensland, Australia; a region with a variety of human land uses. Pollutants in yellowfin bream were best explained by the extent of intensive uses in the catchment. Pollutants in mud crabs were best explained by the extent of irrigated agriculture and water bodies. No samples contained detectable levels of pesticides, and only six samples contained low levels of PFASs. Metals were common in fish and crab flesh, but only mercury in yellowfin bream from the Mooloolah River breached Australian food safety standards. High pollutant presence and concentration is not the norm in seafood collected during routine surveys, even in estuaries with highly modified catchments.