Background: Outdoor air comprises a complex mixture of biological particles that are released in different seasons, weather and time of day. Understanding temporal changes in airborne fungal communities helps interpret their ecological roles and impact on crop health. Here, we describe sampling and metabarcoding approaches to characterise seasonal variation in airborne fungal communities at a rural agricultural site. Methods: Rotorod spore traps collected weekly samples above wheat, oilseed rape, and bare fallow plots at 0.5 m and 2.5 m, or 1m heights above ground during spring and autumn over three years, alongside a 10m roof-level sampler. DNA was extracted from samples, the fungal ITS region was amplified by PCR and sequenced using an Oxford Nanopore MinION. Community structure and species richness was compared bioinformatically across crops, heights, fields, and seasons. Results: Marked seasonal differences in airborne fungal community composition were observed. Autumn communities were characterised by a higher relative abundance of basidiomycetes and saprotrophic taxa, whereas spring communities contained a greater proportion of ascomycetes and plant-pathogens. Co-occurrence networks were visualised in R using igraph and ggraph, with nodes representing fungal genera and edges representing significant correlations. Network topology metrics were used to compare structural complexity and organisation between seasons. Conclusions: Seasonal restructuring of the aerobiome can be characterised using community co-occurrence network approaches. Differences between small (24 m × 24 m) crop plots were relatively minor, indicating a strong background component of the airborne fungal community, highlighting  important considerations for biodiversity monitoring and pathogen surveillance using air-sampling.