Monolayer protected nanoparticles (NPs) include an inorganic core and a monolayer of organic ligands. The wide variety of core materials and the tunable surface monolayers make NPs promising materials for numerous applications. Concerns related to unforeseen human health and environmental impacts of NPs have also been raised. In this thesis, new analytical methods based on mass spectrometry are developed to understand the fate, transport, and biodistributions of NPs in the complex biological systems. A laser desorption/ionization mass spectrometry (LDI-MS) method has been developed to characterize the monolayers on NP surface. LDI-MS allows multiple NPs taken up by cells to be measured and quantified in a multiplexed fashion. The correlations between surface properties of NPs and cellular uptake have also been explored. LDI-MS is further coupled with inductively coupled plasma mass spectrometry (ICP-MS) to quantitatively measure monolayer stability of gold NPs (AuNPs) and quantum dots (QDs), respectively, in live cells. This label-free approach allows correlating monolayer structure and particle size with NP stability in various cellular environments. Finally, uptake, distribution, accumulation, and excretion of NPs in higher order organisms, such as fish and plants, have been investigated to understand the environmental impact of nanomaterials. The results indicate that surface chemistry is a primary determinant. NPs with hydrophilic surfaces are substantially less toxic and present a lower degree of bioaccumulation, making these nanomaterials attractive for sustainable nanotechnology.