Weeds in agricultural landscapes can serve as alternate hosts for phytopathogenic fungi and promote the spatial and long-term distribution of these fungi. Especially, semi-natural habitats such as kettle holes are considered as a source of fungal pathogens because they are a permanent habitat for various weed species in arable lands. In our study, we investigated the suitability of nine different weed species and families at the edges of 18 kettle holes in two consecutive autumn/winter seasons as alternate hosts for Fusarium and Alternaria. We detected a fungal infestation with both genera on every weed species investigated with significantly higher abundances of these fungi in the second, notably wetter season. Eight weed species were described as non-host plants for Fusarium and Alternaria in agricultural landscapes in Brandenburg, Germany for the first time. In both autumn/winter periods, weeds harbored more Alternaria than Fusarium. The study revealed a high Fusarium species diversity in weeds and a community structure of up to 12 Fusarium species at the edges of kettle holes. Grasses showed the highest diversity and often the highest fungal abundances compared to herbaceous plants. Therefore, these habitats in arable lands can act as ecosystem disservice and promote the spread of fungal diseases in the surrounding crop fields.