In this study, the results of the analysis of Pu-238 and Pu-239 + 240 activity concentrations on aerosol filters collected from 2010 to 2016 in Krakow (Southern Poland) are presented and discussed. For the first time, the temporal variation of Pu-239 + 240 activity concentration in surface air in Poland was studied using Fourier analysis. The analysis clearly showed that the Pu-239 + 240 content in the near-ground air layer is subject to seasonal variations and demonstrates annual periodicity. Pu analyses were performed using alpha spectrometry. The measured values ranged from 1.93∙10−10 Bq/m3 to 1.31∙10−8 Bq/m3 with an average of 2.07∙10−9 Bq/m3 for Pu-239 + 240 and from 9.07∙10−11 Bq/m3 to 1.27∙10−9 Bq/m3 with the average 1.52∙10−10 Bq/m3 for Pu-238. The analysis of the potential sources of plutonium isotopes in the air aerosols samples indicated that only two samples are uniquely characterized by the ratio corresponding to spent nuclear fuel: February 2012 (0.59 ± 0.18) and February 2015 (0.68 ± 0.19). The remaining samples showed mixed origins, with global radioactive fallout appearing to contribute more than spent nuclear fuel. To study the relationship between Pu-239 + 240 and meteorological conditions, Pearson's correlation and circulation pattern analyses were performed. The analyses showed that the Pu-239 + 240 activity concentration depends on air temperature (R = 0.51), the sum of ice and snowfall (R = −0.45), relative humidity (R = −0.54) and mean total cloud cover (R = −0.56). High concentrations of Pu-239 + 240 were positively correlated with air advection from the southern and eastern sectors, whereas low concentrations were observed during dynamic weather conditions with intense circulation from the western sector. In case of Pu-238 no significant correlation was observed.