The spawning sites, incubation success, and density of young-of-the-year (YOY) brook trout (Salvelinus fontinalis) were examined in stream populations experiencing varying levels of sediment stress. Our objective was to determine effects on embryos and YOY and examine cumulative effects on the populations. Early development was unaffected (88% survival). Mortality occurred at late, encapsulated embryo stages likely as a function of oxygen deprivation within redds. Survival to emergence from the substrate was significantly reduced (∼50%) in redds in which fine sediments accumulated. Groundwater reduced sediment accumulation in redds and enhanced survival. Sediment may have affected dispersal of YOY trout. All populations appeared successful in term of total density (average = 72/100 m²). Our findings emphasize the importance of targeting multiple life-history stages and understanding local adaptations when searching for true population-level effects in any stressed ecosystem.