We investigated the impacts of spherical and triangular-plate-shaped lipid-coated silver nanoparticles (AgNPs) designed to prevent surface oxidation and silver ion (Ag+) dissolution in a small-scale microcosm to examine the role of shape and surface functionalization on biological interactions. Exposures were conducted in microcosms consisting of algae, bacteria, crustaceans, and fish embryos. Each microcosm was exposed to one of five surface chemistries within each shape profile (at 0, 0.1, or 0.5 mg Ag/L) to investigate the role of shape and surface composition on organismal uptake and toxicity. The hybrid lipid-coated AgNPs did not result in any significant release of Ag+ and had the most significant toxicity to D. magna, the most sensitive species, although the bacterial population growth rate was reduced in all exposures. Despite AgNPs resulting in increasing algal growth over the experiment, we found no correlation between algal growth and the survival of D. magna, suggesting that the impacts of the AgNPs on bacterial survival influenced algal growth rates. No significant impacts on zebrafish embryos were noted in any exposure. Our results demonstrate that the size, shape, and surface chemistry of AgNPs can be engineered to achieve specific goals while mitigating nanoparticle risks.