Many studies have shown that biodiversity regulates multiple ecological functions that are needed to maintain the productivity of a variety of ecosystem types. What is unknown is how human activities may alter the 'multifunctionality' of ecosystems through both direct impacts on ecosystems and indirect effects mediated by the loss of multifaceted biodiversity. Using an extensive database of 72 lakes spanning four large Neotropical wetlands in Brazil, we demonstrate that species richness and functional diversity across multiple larger (fish and macrophytes) and smaller (microcrustaceans, rotifers, protists and phytoplankton) groups of aquatic organisms are positively associated with ecosystem multifunctionality. Whereas the positive association between smaller organisms and multifunctionality broke down with increasing human pressure, this positive relationship was maintained for larger organisms despite the increase in human pressure. Human pressure impacted multifunctionality both directly and indirectly through reducing species richness and functional diversity of multiple organismal groups. These findings provide further empirical evidence about the importance of aquatic biodiversity for maintaining wetland multifunctionality. Despite the key role of biodiversity, human pressure reduces the diversity of multiple groups of aquatic organisms, eroding their positive impacts on a suite of ecological functions that sustain wetlands.