California produces 99% of the nation’s processing tomatoes and 26% of global production. Due to increasing water scarcity, deficit irrigation (DI) is a common practice in which growers irrigate to replace only a fraction of evapotranspiration (ET) needs starting at fruit ripening. However, this practice may enhance losses from soil borne diseases. This work attempted to enable the use of DI under disease pressure by first evaluating its cumulative effects on soil borne disease development, water stress, plant nutrition, and yields in a naturally infested field and determining if soil management practices can influence DI impacts on plant health (Chapter 1). We observed increased disease symptoms (vine decline, stem rot, and reduced red marketable fruit) under DI. Fusarium oxysporum f. sp. radicis-lycopersici (Fusarium crown and root rot, Forl) and F. noneumartii (Fusarium stem rot and vine decline, FRD) were the predominant pathogens isolated. The latter was isolated only from plants grown in the DI treatment, suggesting disease enhancement of this pathogen under DI. Because fungicides do not effectively manage soil borne pathogens and methyl bromide fumigation is highly restricted, we wanted to determine if cultivar-based management is effective in reducing disease development and yield losses under DI. We examined the effects of DI FRD in four cultivars with putative tolerance and evaluated whether greater FRD sensitivity under DI was related to water stress tolerance traits (Chapter 2). We observed enhanced FRD disease development under DI and found that cultivars with better water stress tolerance performed better under DI and FRD disease pressure indicating that appropriate cultivar selection can be a useful management tool. To better understand the microbial basis for increased disease symptoms under DI we used culture-dependent methods and amplicon sequencing to explore possible enhancement of soil borne pathogens under two DI treatments and to determine the effects of composted soil amendments and cover cropping on fungal root microbial communities; additionally, putative facultative Fusarium pathogens dominant in the ecosystem were tested for pathogenicity (Chapter 3). Fusarium brachygibbosum isolates caused stem lesions on seedlings, suggesting that it is a facultative pathogen of tomato. With amplicon sequencing, we did not observe an effect of DI on fungal diversity or abundance, however we did observe an effect of compost amendment and cover cropping. Characterization of bacterial root microbial communities is forthcoming and may provide us with a better understanding of the effects of DI and soil management. Overall, this work confirms that DI can enhance losses caused by soil borne disease and informs management decisions regarding the importance of appropriate cultivar selection and soil management techniques for growers facing reduced water allocations and disease pressure.