Shallow lakes in subtropical climate regions may have a clear water state with a predominance of submerged or floating macrophytes and a turbid water state with a predominance of phytoplankton. The relationship between microcrustaceans and these changes in alternative states is still incipient in the literature. And to better understand these relationships, the functional approach is an excellent tool. Thus, the present work seeks to test the hypothesis that changes in alternative stable states over time reflect the variability of composition and functional diversity of microcrustaceans. For this, samples of microcrustaceans collected in a subtropical shallow lake, which underwent alternate state changes in the period to 2000-2014, were used. Our results demonstrate a variation in composition and functional diversity among alternative states, thus supporting our hypothesis. In periods of clear water with a predominance of floating macrophytes, we found a greater functional diversity and richness of genera. This result may be associated with several factors such as greater habitat heterogeneity and lower predation pressure. The lowest values of functional diversity found in periods of turbid waters with predominance of phytoplankton and periods of clear waters with submerged macrophytes are related to the dominance of functional traits, such as scraper feeding type, herbivorous/omnivorous trophic group, littoral habitat and asexual reproduction. These traits are functional features of most Ostracoda genera, a taxonomic group abundant in these two alternative states. The predominance of this group may be related to the environmental characteristics of these periods, such as the high vegetation cover and the availability of niches unoccupied by more sensitive species, since most Ostracoda have high environmental tolerance. We conclude that the functional traits approach combined with taxonomic groups respond to temporal variations of alternative stable states and are important tools to detect environmental changes.