Substrate type modulates tomato yield and fruit quality under brackish water irrigation: Insights from multivariate and structural equation modeling

• Tomato yield and fruit quality under brackish irrigation are strongly influenced by substrate type. • A commercial soilless substrate maintained higher porosity and supported greater root activity under salinity stress. • Moderate brackish irrigation (3 mS/cm) improved fruit sugar–acid ratio and soluble solids without reducing yield. • Principal component and discriminant analyses revealed substrate as the primary driver of trait variability. • Structural equation modeling identified substrate porosity and root activity as key determinants of yield performance. The sustainable use of brackish water in protected horticulture requires a clear understanding of how substrate properties influence plant responses to salinity. This study evaluated the effects of three irrigation water salinity levels (0,3, and 5 mS/cm) and three cultivation substrates, loamy soil (SO), sandy soil (SA), and commercial substrate (SU), on substrate properties, nutrient dynamics, and tomato ( Solanum lycopersicum L.) growth, yield, and fruit quality. Saline irrigation increased substrate EC, pH, and ion accumulation while reducing porosity and water-holding capacity. SU maintained superior physical structure and nutrient availability, supporting higher root activity and yield across salinity levels. SO showed greater salt retention but suffered substantial yield loss under high salinity. Moderate salinity (3 mS/cm) enhanced sugar–acid ratio and soluble solids content in most substrates. However, vitamin C and nitrate concentrations did not differ significantly among treatments, indicating trait-specific insensitivity to substrate or salinity. Principal Component Analysis (PCA) revealed substrate type as the dominant factor shaping trait variation, while Linear Discriminant Analysis (LDA) separated salinity levels using nine key traits. Structural Equation Modeling (SEM) identified root activity and substrate porosity as major drivers of yield, while ion content influenced fruit quality components. These findings suggest that moderate brackish irrigation, when paired with substrates that enhance root function and nutrient use efficiency, can support sustainable tomato production without compromising quality.