1. Understanding the mechanisms that underlie species assembly is a central concern in community ecology. Abiotic and biotic filters are probabilistic ‘sieves’ that allow species with certain functional traits to become part of the community, or not. We manipulated natural plant assemblieses in order to identify variations in the timings of biotic and abiotic filters that determine community trait assemblies. 2. We extracted soil portions when the investigated annual plant community was in its seed phase (‘community monolith’), thereby maintaining the structure and similar soil characteristics to the field conditions. Community monoliths were subjected to experimental manipulation in terms of the rainfall timing and amount, and perturbations of the biological soil crust (BSC; intact vs. perturbed). We surveyed the experimental community assembly over time based on the functional diversity by considering important functional traits in different life stages. 3. We found that autumn droughts acted as abiotic filters by favouring the germination and establishment of species with greater investment in the root biomass. Under severe droughts (66% water reduction), the experimental assemblies were dominated by species with functional traits adapted to water shortage conditions: high leaf dry matter content, low specific leaf area, small individual size, low reproductive ratio, and high root:shoot ratio. We identified two roles of BSCs in annual plant species assemblies: 1) as a biotic filter that limited the establishment of species based on seed size, and 2) as a buffer against water stress conditions by reducing soil evapotranspiration. 4. Synthesis. We demonstrated the importance of the timing and amount of rainfall for shaping annual plant communities, and identified germination filters as the main process that determined community assemblies. Our results suggest that the phenotypic integration of functional traits facilitates resistance to drought during the life cycle. The BSC–annual plant relationship shifted from negative by acting as a germination filter to positive by acting as a buffer in later stages. Climatic fluctuations and fine scale biotic determinants of spatial heterogeneity emerged as sources of changes in the community assembly in time and space to possibly promote species coexistence and trait differences among the communities studied.