Coccidioidomycosis is a typically respiratory fungal disease that, in the United States, occurs primarily in Arizona and California. In California, most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily agricultural region where the disease poses a risk for outdoor workers. We collected 710 soil samples and 265 settled dust samples from nine sites in the San Joaquin Valley and examined howCoccidioidesdetection varied by month, site, and the presence and abundance of other fungal species. We detectedCoccidioidesin 89 of 238 (37.4%) rodent burrow soil samples at five undeveloped sites and were unable to detectCoccidioidesin any of 472 surface and subsurface soil samples at four agricultural sites. In what is the largest sampling effort undertaken on agricultural land, our results provide no evidence that agricultural soils in the San Joaquin Valley harborCoccidioides. We found no clear association betweenCoccidioidesand the greater soil fungal community, but we identified 19 fungal indicator species that were significantly associated withCoccidioidesdetection in burrows. We also did not find a seasonal pattern inCoccidioidesdetection in the rodent burrow soils we sampled. These findings suggest both the presence of a spore bank and that coccidioidomycosis incidence may be more strongly associated withCoccidioidesdispersal thanCoccidioidesgrowth. Finally, we were able to detectCoccidioidesin only five of our 265 near-surface settled dust samples, one from agricultural land, whereCoccidioideswas undetected in soils, and four from undeveloped land, whereCoccidioideswas common in the rodent burrow soils we sampled. Our ability to detectCoccidioidesin few settled dust samples indicates that improved methods are likely needed moving forward, though raises questions regarding aerial dispersal inCoccidioides, whose key transmission event likely occurs over short distances in rodent burrows from soil to naïve rodent lungs.