Recent studies have shown that local variation in sediment geochemistry can have significant effects on settlement rates of benthic invertebrates. For example, elevated porewater ammonium concentrations in soft-sediment benthic systems may result in decreased recruitment rates of settling larvae. Recruitment responses of the benthic polychaete Arenicola cristata and the bivalve Mercenaria mercenaria to varying ammonium concentrations were measured in realistic flow environments. Experiments made novel use of ammonium-spiked polyacrylamide gels placed beneath field-collected sediment, which produced predictable porewater ammonium concentrations. Post-larval arenicolids and Mercenaria were allowed to settle in an annular flume containing sediment treatments with varying ammonium concentrations. Porewater ammonium data indicated successful manipulation of geochemical properties without contamination of overlying water. In Mercenaria trials, recruit retention was low. For Arenicola trials, significant retention differences were observed as a function of ammonium concentration, and indicate that ammonium plays a significant role in determining recruitment patterns and hence juvenile abundance.