Workers from specific occupational settings may be exposed to high fungal bioaerosol concentrations, causing detrimental health effects. Therefore, we conducted a study to evaluate the characteristics and health effects of fungal bioaerosols present on agricultural farms. By using IOM inhalable dust samplers, personal and area samples of airborne fungi were collected from five agricultural farms—two mushroom and three vegetable farms. A standardized questionnaire and spirometry were used to evaluate workers’ health. The Kruskal–Wallis test was used to examine the distributions of fungal and environmental factors among the different farms, and regression analyses were performed to evaluate the effects of personal bioaerosol exposure on workers’ health. In the personal samples, the geometric mean concentrations ranged from 4.3 × 103 to 3.0 × 104 CFU m–3 for total culturable fungi and from 4.2 × 103 to 1.2 × 105 spores m–3 for total fungal spores. The total fungal spore concentrations differed significantly among the personal samples (p = 0.026), but not among the area samples, from the five farms. The culturable fungal concentrations among the five farms did not differ significantly in the personal or area samples. Decreased lung functions of the workers were significantly associated with the concentrations of total fungi and several fungal taxa such as Ascospores, Fusarium, and Periconia. This study demonstrated that exposure to high fungal bioaerosol concentrations reduced the lung functions of the mushroom and vegetable farm workers. Superior ventilation and appropriate personal protection equipment are required to reduce occupational biohazards.