To test the effects of habitat fragmentation per se on the survival and growth of the northern quahog (Mercenaria mercenaria Linné), we stocked juvenile quahogs in 10 seagrass patches (Halodule wrightii Ascherson) ranging in size from 0.5–1,750 m2 for two consecutive months during the summer of 2004. As a control, additional quahogs were stocked in cages located in seagrass patches that spanned the same size range. We tested for changes in shell growth, somatic growth, and mortality between caged and non-caged treatments and we estimated the strength of linear relationships between all three measures of growth and mortality with patch area, perimeter, perimeter: area ratio, seagrass aboveground biomass, and epiphyte biomass. Shell and somatic growth were each significantly greater in cages, whereas mortality was significantly less than in uncaged treatments. There were no significant relationships between clam mortality and either patch perimeter, seagrass above ground biomass, or epiphyte biomass, but during July only there was a negative relationship between clam mortality and patch area. Patch area, perimeter, perimeter: area ratio, and seagrass aboveground biomass each had some significant influence on either changes in shell height, length, or somatic growth; but this influence varied between the two trials. Our data suggest that the influence of habitat fragmentation per se declined from June to July, which may the result of increasing predator densities and changes in seagrass patch characteristics.