Globally, anthropogenic activities have degraded many estuarine habitat types, including seagrass meadows. The objective of this study was to identify the degree to which light and nutrients limit the productivity of eelgrass Zostera marina in Long Island estuaries (NY, USA) while concurrently assessing the ability of hard clams Mercenaria mercenaria to influence Z. marina growth and production. Field surveys were conducted to quantify the extent of eelgrass beds, along with environmental factors potentially constraining eelgrass growth. Experimental studies were conducted to determine the extent to which eelgrass is light- or nutrient-limited within the system, and to determine the capacity of hard clams to enhance eelgrass growth in situ. Eelgrass was found in only 14% of the sites sampled, but hard clams were found in 67% of sites with eelgrass. There was a strong longitudinal light gradient in Shinnecock Bay, with an extinction coefficient of 0.88 at the ocean inlet and 2.05 in the most remote regions. Pelagic light levels were inversely correlated with water column chlorophyll levels (p = 0.0027) and eelgrass productivity was strongly correlated with light levels (p < 0.0004), with both being maximal near the ocean inlet. In estuarine regions with high light levels but significantly lower sediment nitrogen (N) content (near ocean inlet), hard clam or sediment nutrient additions yielded significantly higher eelgrass productivity and leaf N content (p < 0.001) compared to control plots. Combined with prior research, this study demonstrates that restoration of bivalves may benefit the expansion of eelgrass beds in shallow estuaries by relieving light and/or nutrient limitation.