Post-settlement survival and growth of bivalves can be limited by abiotic and biotic factors, both of which are spatially variable. Rarely has the importance of these factors been tested concurrently in the field. Our study spanned three spatial scales in estuarine waters of Washington state (Region: north vs. south; Within-region: fresher vs. saline; Within-site: mid- vs. low-tidal elevation). Predator access and sediment conditions were manipulated in a crossed experimental design, with juvenile (3-mm and 6-mm) Manila clams (Ruditapes philippinarum) outplanted in open- or closed-top mesh tubes. We found differences between treatments that appeared only at sites with cancrid crabs, suggesting that predators, rather than emigration, likely reduced numbers of clams in open tubes. We had hypothesized that clams at lower tidal elevations, which experience longer immersion times, would show improved growth but reduced survivorship because of greater exposure to marine predators. However, these patterns were evident at only one of three sites (lower-elevation treatments were lost at the fourth). The larger size class of clams was more tolerant of abiotic stressors at all sites, but the magnitude of difference in survival between size classes was sometimes dependent on other treatments. The maximum predator effect on survival was 74% (north, high salinity, low-intertidal site), whereas the maximum abiotic effect appeared as 62% lower survival and 59% slower growth for 3-mm clams at another site (north, fresher). In laboratory trials, high water temperatures (28–32 °C) and low salinity (5–15) acted synergistically to cause juvenile clam (6–12 mm) mortality, whereas clams tolerated each of these stressors alone. Context-dependence in the relative importance of predation and abiotic stressors was apparent in our results, but contrary to expectations, abiotic stressors did not characterize southern or fresher sites. Instead, extreme high temperatures occurred at the site with the wide tidal flat rather than in the south, and the within-region salinity differences appeared not to exceed tolerances of juvenile clams.