Significant progress has been made in understanding the toxicity of silver nanoparticles (Ag NPs) under carefully controlled laboratory conditions. Natural organic matter (NOM) is omnipresent in complex environmental systems, where it may alter the behavior of nanoparticles in these systems. We exposed the nematode Caenorhabditis elegans to Ag NP suspensions with or without one of two kinds of NOM, Suwannee River and Pony Lake fulvic acids (SRFA and PLFA, respectively). PLFA rescued toxicity more effectively than SRFA. Measurement of total tissue silver content indicated that PLFA reduced total organismal (including digestive tract) uptake of ionic silver, but not of citrate-coated Ag NPs (CIT-Ag NPs). The majority of the CIT-Ag NP uptake was in the digestive tract. Limited tissue uptake was detected by hyperspectral microscopy but not by transmission electron microscopy. Co-exposure to PLFA resulted in the formation of NOM–Ag NP composites (both in medium and in nematodes) and rescued AgNO3- and CIT-Ag NP-induced cellular damage, potentially by decreasing intracellular uptake of CIT-Ag NPs.