Esca disease and Botryosphaeria dieback are currently considered as serious grapevine diseases which affect vineyard health and induce economic losses. Both of these trunk diseases (GTDs) are caused by a complex of pathogens, and foliar expression is influenced by several factors, including environmental factors such as water stress. To manage water stress in some vine areas, culture practice based on irrigation systems for limiting water stress have been developed; however, little knowledge of the influence of such systems on GTD emergence is currently available. The present paper addresses the impact of irrigation systems and climatic factors (rainfall and temperature) on the expression of GTDs, specifically esca and Botryosphaeria dieback. A field experiment on Chardonnay in North East Spain, a vine growing area where drought is present and which is managed by an irrigation system, was therefore carried out during a 3-year period. The water stress impact on GTD expression was evaluated by measuring the GTD incidence and analysing different physiological parameters at different phenological stages, including principal component analysis and gene expression. The main finding of this study was the significant roles of vine transpiration and water availability, which depend on irrigation volume and rainfall amount; together, they may explain the erratic symptom expression in plants infected by GTD fungi depending on the year. All these parameters are discussed to better understand the relationship between GTD expression, irrigation system and climatic factors.