Different measures of macroinvertebrate diversity (species diversity, functional diversity, phylogenetic diversity) and functional feeding groups (FFGs) are commonly used to assess the ecological status of large shallow lakes. In this study, biodiversity and FFGs in a large shallow lake, Lake Hongze, differed between littoral and pelagic habitats, with the spatial variability of littoral assemblages more correlated with nutrient concentrations, whilst pelagic assemblages were more associated with wave-induced disturbance (e.g., mean effective fetch). Species diversity was poorly correlated with measures of nutrient concentrations, whereas functional diversity, phylogenetic diversity and functional feeding groups are promising indicators of nutrient concentrations. Multimetric indexes (MMI) were developed for both habitats, using historical data as reference for pelagic and least disturbed conditions for littoral. Key attributes for pelagic MMI included Biological Monitoring Working Party (BMWP), mollusca taxa, and the percentage of mollusca taxa, the percentage of filter-collector taxa, the percentage of predator taxa, the percentage of gather-collector taxa, the percentage of sensitive taxa and functional dispersion, while littoral MMI incorporated the percentage of scraper abundance, mollusca taxa, Biological Pollution Index and BMWP. The results of structural equation models (SEM) indicated that sediment organic matter strongly affected pelagic health, while chlorophyll a and transparency influenced littoral health due to varying littoral utilization. The study supports using biodiversity and FFGs to understand nutrient and disturbance effects on macroinvertebrates. Furthermore, monitoring both littoral and pelagic habitats in large shallow lakes is recommended for comprehensive ecosystem assessment.