Similarities and differences of phenotypes within local co-occurring species hold the key to inferring the contribution of stochastic or deterministic processes in community assembly. Developing both phylogenetic-based and trait-based quantitative methods to unravel these processes is a major aim in community ecology. We developed a trait-based approach that: (i) assesses if a community trait clustering pattern is related to increasing environmental constraints along a gradient; and (ii) determines quantitative thresholds for an environmental variable along a gradient to interpret changes in prevailing community assembly drivers. We used a regional set of natural shallow saline ponds covering a wide salinity gradient (0.1-40% w/v). We identify a consistent discrete salinity threshold (ca. 5%) for microbial community assembly drivers. Above 5% salinity a strong environmental filtering prevailed as an assembly force, whereas a combination of biotic and abiotic factors dominated at lower salinities. This method provides a conceptual approach to identify consistent environmental thresholds in community assembly and enables quantitative predictions for the ecological impact of environmental changes.