Pollen and molds are environmental allergens that are affected by climate change. As pollen and molds exhibit geographical variations, we sought to understand the impact of climate change (temperature, carbon dioxide (CO(2)), precipitation, smoke exposure) on common pollen and molds in the San Francisco Bay Area, one of the largest urban areas in the United States. When using time-series regression models between 2002 and 2019, the annual average number of weeks with pollen concentrations higher than zero increased over time. For tree pollens, the average increase in this duration was 0.47 weeks and 0.51 weeks for mold spores. Associations between mold, pollen and meteorological data (e.g., precipitation, temperature, atmospheric CO(2), and area covered by wildfire smoke) were analyzed using the autoregressive integrated moving average model. We found that peak concentrations of weed and tree pollens were positively associated with temperature (p < 0.05 at lag 0-1, 0-4, and 0-12 weeks) and precipitation (p < 0.05 at lag 0-4, 0-12, and 0-24 weeks) changes, respectively. We did not find clear associations between pollen concentrations and CO(2) levels or wildfire smoke exposure. This study's findings suggest that spore and pollen activities are related to changes in observed climate change variables.