Fusarium head blight (FHB) is a global problem in small-grains agriculture that results in yield losses and, more seriously, produces harmful toxins that enter the food chain. This study builds on previous research identifying within-field humidity as an important factor in infection processes by Fusarium species and its mycotoxin production. Environmental variables describing topographic control of humidity (TWI), soil texture and related moisture by electrical conductivity (ECa), and canopy humidity by density (NDVI) were explored in their relationship to the fungal infection rates, the abundance of trichothecene-producing Fusarium spp. as determined by TRI 6 gene copies and mycotoxin accumulation. Field studies were performed at four field sites in northeastern Germany in 2009 and 2011. In the wet year 2011, a high Fusarium infection rate resulted in a high abundance of trichothecene-producing fungi as well as high concentrations of mycotoxins. Simultaneously, Fusarium spp. inhibited the development of other filamentous fungi. Overall, a very heterogeneous distribution of pathogen infections and mycotoxin concentrations were displayed in each field in each landscape. The NDVI serves as an important predictor of the occurrence of phytopathogenic Fusarium fungi and their mycotoxins in a field and landscape scale. In addition, the ECa reflects the distribution of the most frequently occurring mycotoxin deoxynivalenol within the fields and landscapes. In all cases, TWI was not found to be a significant variable in the models. All in all, the results extend our knowledge about suitable indicators of FHB infection and mycotoxin production within the field.