Recent studies have shown that local variation in surface sediment geochemistry can have significant effects on recruitment rates of benthic invertebrates. Experiments presented here tested (1) the utility of manipulating surface porewater concentrations using spiked polyacrylamide gels and (2) the recruitment responses of the polychaete Arenicola cristata and the bivalve Mercenaria mercenaria to manipulated ammonium concentrations in realistic flows provided by a straight flume and an annular flume. Data show that successful manipulation of sediment porewater ammonium concentration is feasible in flowing waters, i.e., overlying waters remained relatively free of ammonium while manipulated concentration levels were maintained within the upper sediment layers where new recruits explore. Thus, over short experimental periods, ammonium signals can be independently modified while variables such as grain size, organic content and flow are held constant. Responses of new recruits varied as a function of experimental condition. In straight flume trials, the manipulation of ammonium concentration was successful, and within the range of concentrations tested, retention of Mercenaria was significantly reduced at the highest ammonium level. However, retention of Arenicola was uniformly low among all treatments and no significant ammonium response was detected. In annular flume runs, overall ammonium concentrations were higher than in straight flume runs, but were consistent with the intended manipulation. Mercenaria retention was uniformly low, and no differences in retention, as a function of ammonium concentration, were found. However, for Arenicola, significant differences were observed, with highest retention in lower ammonium environments. These results suggest that ammonium, isolated from other cues, plays a significant role in determining recruitment patterns, with variation in recruit responses related to signal strength.