Understanding how functional traits distributed across ecological scales as well as environmental gradients are central issues of trait-based assembly processes. However, whether environmental filters act on individuals or species mean traits remains poorly tested. Here, we measured four functional traits - shoot height, specific leaf area, lamina thickness, and leaf dry mass content - of 4432 individuals from 30 submersed macrophyte species across 26 lakes in south China, covering a broad nutrient gradient. We partitioned trait variances into four nested ecological scales (i.e., region, community, species, individual) and assessed how the internal and external filters structured the submersed macrophyte community, either through acting on individual or on species mean traits, and how these processes related to nutrient enrichment. For the four tested traits, 13-60% of trait variability occurred within species (individual level), while 35-86% occurred among species (species level), followed by community and regional level. Species turnover contributed most to the community-wide variance along the nutrient gradient caused considerable intraspecific variations of shoot height. We found significant strong internal filtering effects on the submersed macrophyte community, which increased towards higher nutrient levels. The external filtering effects were only observed at individual level, with lower shoot height, specific leaf area, and leaf dry mass content than expected at low nutrient levels, and lower lamina thickness than expected at high nutrient levels. Our study provides new insight into the assembly processes by showing that niche overlap (i.e., intraspecific interaction) and niche differentiation (i.e., interspecific interaction) can simultaneously occur in different functional traits, both potentially promoting local species diversity. We conclude that an individual trait-based approach can help to detect assembly processes within and among lakes.