Air pollution is a global issue that leads to various negative outcomes to human health and the environment. Particulate matter in the air, especially that with an equivalent aerodynamic diameter of less than 10 μm (PM10) and 2.5 μm (PM2.5), has been proven to have harmful effects and can contain various toxic substances. Polycyclic aromatic hydrocarbons (PAHs) are compounds of particular interest due to their harmful carcinogenic effects, while polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) belong to the group of persistent organic pollutants characterized by persistence, bioaccumulation, and toxicity. Atmospheric deposition, including dry and wet deposition, is crucial for removing pollutants from the air, but it can have negative effects on ecosystems and, indirectly, on human health. Harmful organic compounds enter the soil through natural deposition processes, as well as due to local events such as oil spills, improper waste disposal, and fires. In the first part of this study, preliminary investigations were conducted, covering various sample preparation methods for determining PAHs, PCBs, and OCPs in particulate matter, total deposited matter (TDM), and soil. Procedures that showed optimal results for the simultaneous determination of all three groups of compounds were selected. The optimized methods were applied to samples of PM10, TDM, and soil at various polluted locations in the city of Zagreb and its surroundings. Over three years (2020–2023), monthly TDM samples were continuously collected at ten locations, and weekly samples of the PM10 fraction of airborne particles were collected at one measurement site in 2022. Additionally, composite samples of the surface soil layer were collected at the same locations in 2022, and the physical and chemical characteristics of the soil and the elements present were determined. Differences in PAHs deposition fluxes between measurement sites were found, but were statistically significant only for PAHs with 4 aromatic rings and benzo[a]pyrene in TDM at some locations. No statistically significant difference between locations was found for PCBs and OCPs in TDM. Significant seasonal differences in deposition fluxes were observed for PAHs, some hexa- and hepta-PCBs, and HCH isomers, with the highest values recorded in winter. The mass concentrations of PAHs, HCH, DDT and its degradation products in the PM10 were significantly higher in winter, while the seasonal minimum and maximum for PCBs differed depending on the chlorination degree of the compound. The diagnostic ratios of PAHs and results of factor analysis, cluster analysis, and principal component analysis indicated the presence of different pollution sources, depending on the location and season (biomass burning, petroleum and fossil fuel combustion, traffic emissions), while PCBs and OCPs were associated with historical or transboundary inputs. The applied statistical tools indicated complex relationships between compounds and differently grouped locations depending on the observed environmental compartment. In addition to local sources, the geographical location of the measurement site also affects the levels of PAHs, PCBs, and OCPs, likely related to different precipitation regimes and airflow patterns. Significant linear correlation between PAHs in TDM and PM10, as well as between PCBs with higher degrees of chlorination in TDM and PM10, suggested that dry deposition likely played a significant role in removing these compounds from the atmosphere. Relationships between individual PAHs, PCBs, and OCPs in soil and TDM indicated the complex circulation mechanisms of these compounds in the environment.