Subterranean clover (Trifolium subterraneum) is a critical pasture legume in Mediterranean regions of southern Australia and elsewhere, including Mediterranean-type climatic regions in Africa, Asia, Australia, Europe, North America, and South America. Pythium damping-off and root disease caused by Pythium irregulare is a significant threat to subterranean clover in Australia and a study was conducted to define how environmental factors (viz. temperature, soil type, moisture and nutrition) as well as variety, influence the extent of damping-off and root disease as well as subterranean clover productivity under challenge by this pathogen. Relationships were statistically modeled using linear and generalized linear models and boosted regression trees. Modeling found complex relationships between explanatory variables and the extent of Pythium damping-off and root rot. Linear modeling identified high-level (4 or 5-way) significant interactions for each dependent variable (dry shoot and root weight, emergence, tap and lateral root disease index). Furthermore, all explanatory variables (temperature, soil, moisture, nutrition, variety) were found significant as part of some interaction within these models. A significant five-way interaction between all explanatory variables was found for both dry shoot and root dry weights, and a four way interaction between temperature, soil, moisture, and nutrition was found for both tap and lateral root disease index. A second approach to modeling using boosted regression trees provided support for and helped clarify the complex nature of the relationships found in linear models. All explanatory variables showed at least 5% relative influence on each of the five dependent variables. All models indicated differences due to soil type, with the sand-based soil having either higher weights, greater emergence, or lower disease indices; while lowest weights and less emergence, as well as higher disease indices, were found for loam soil and low temperature. There was more severe tap and lateral root rot disease in higher moisture situations.