Fusarium crown rot (FCR), caused by the fungal pathogen Fusarium pseudograminearum (Fp), is a major constraint to cereal production worldwide. The pathogen restricts the movement of solutes within the plant due to mycelial colonisation of vascular tissue. Yield loss and quality downgrades are exacerbated by this disease under water stress conditions. Plant root systems are adaptive and can alter their architecture to optimise production in response to changes in environment and plant health. This plasticity of root systems typically favours resource acquisition of primarily water and nutrients. This study examined the impact of FCR on the root system architecture of multiple commercial bread and durum wheat varieties. Root system growth was recorded in-crop in large transparent rhizoboxes allowing visualization of root architecture over time. Furthermore, electrical resistivity tomography was used to quantify spatial root activity vertically down the soil profile. Results demonstrated a significant reduction in the total root length and network area with the inoculation of FCR. Electrical resistivity measurements indicated that the spatial pattern of water use for each cultivar was influenced differently from infection with FCR over the growing season. Specifically temporal water use can be correlated with FCR tolerance of the varieties marking this investigation the first to link root architecture and water use as tolerance mechanisms to FCR infection. This research has implications for more targeted selection of FCR tolerance characteristics in breeding programs along with improved specific varietal management in-crop.