Ammonia (NH3) volatilization is one of the main pathways of nitrogen (N). The aim of this work was to investigate the determinants of NH3 volatilization, and characterize how the overlying water, sediment, and periphyton interact to regulate the rates of NH3 volatilization in shallow aquatic systems. Two types of structural equation modeling (SEM) methods ('elements' and 'components' models) were evaluated to examine the complex multivariate response of NH3 volatilization. The N components and the pH in the 'elements' models exerted significant and positive effects on NH3 volatilization. The water column accounted for the greatest variation of NH3 volatilization in a favorable pH environment and high NH4+-N concentrations according to the 'components' models. Although periphyton biofilm prohibited the direct flow of NH3 gas, this was counter-balanced by its indirect stimulation effects that positively affected the NH4+-N and DOC concentrations and the pH in both the overlying water and the sediment.