Nutrient over-enrichment can produce adverse ecological effects within coastal ecosystems and negatively impact the production of ecosystem goods and services. In small estuaries of the U.S. Pacific Northwest, seasonal blooms of green macroalgae (GMA; Ulva spp.) are primarily associated with natural nutrient input, rather than anthropogenic sources. This provided us a unique opportunity to investigate the effects of naturally-stimulated macroalgae blooms on intertidal bivalves. Clinocardium nuttallii (heart cockles) are an important shellfisheries species in the region. In summer population surveys, we found that cockles emerged from the sediment with greater frequency as GMA biomass increased. Experimental manipulation of GMA biomass in the field showed that GMA elicited emergence, evoked above-ground lateral movement, inhibited shell growth, and increased mortality (by 34.0 ± 15.2%) in shell growth, and increased mortality (by 34.0 ± 15.2%) in cockles. Laboratory experiments revealed that the interaction of a weighted barrier at the sediment surface and GMA presence elicited rapid emergence among cockles. Risk assessment of the emergence response in cockles showed that the in-situ emergent population experienced 11.0 ± 8.0% mortality due to gull predation, while laboratory exposure to elevated temperatures (≥34 °C) slowed valve-closure, inhibited reburial, and increased mortality, which could have translated to 7.1 ± 1.5% in-situ mortality. We found that cockles were capable of avoiding mortality due to burial below GMA mats by emerging from the sediment, but that behavior consequently put them at risk of mortality due to heat stress or gull predation. Regardless of nutrient source, our research showed that GMA blooms pose a threat to the survival of intertidal bivalves.