Earthen shrimp aquaculture ponds are often impacted by acid sulfate soils (ASS), typically resulting in increased disease and mortality of cultured organisms. Production losses have been attributed to either low pH or to elevated concentrations of toxic metals, both direct products of pyrite oxidation in ASS. The standard farm management practice to minimise effects of pyrite oxidation is to maintain pH of pond waters above 5, based on the assumption that dissolved metal bioavailability is negligible at this pH. This study aimed to test the validity of this assumption, and therefore elucidate a possible role of toxic heavy metals in observed decreases in farm productivity. Metal bioaccumulation in four genera of macroalgae, Ulva sp., Enteromorpha sp., Cladophora sp. and Chaetomorpha sp., sampled from ASS-affected shrimp aquaculture ponds were measured using inductively coupled plasma-optical emission spectroscopy (ICP-OES) to assess the relative bioavailability of dissolved metals within the system. Results showed that all four genera of macroalgae accumulated appreciable quantities of Fe, Al, Zn, Cd, Cu, As and Pb. Iron and Al, the most common metals mobilised from ASS, were both accumulated in all algal genera to concentrations three orders of magnitude greater than all other metals analysed. These findings indicate that dissolved heavy metals are indeed bioavailable within the aquaculture pond system. A literature search of heavy metal bioaccumulation by these algal genera revealed concentrations recorded in this study are comparable to highly contaminated environments, such as those exposed to urban, industrial and mining pollution. The results of this study indicate that dissolved metal bioavailability in many earthen shrimp aquaculture ponds may be higher than previously thought.