Abstract The alteration of the natural environment by human activities has increased in recent decades, with a significant impact on the organisms that inhabit it. One of the most apparent consequences of environmental alterations is the occurrence of climatic changes. The city of Joinville is situated in the southern region of Brazil. It has achieved a notable position at the national level, largely due to the significant presence of large-scale industrial operations in the metal-mechanical, plastic, and textile sectors. This study aimed to assess the effects of urban environments on Nectandra oppositifolia plants and lichen communities using a passive biomonitoring approach, and on Tetragonisca angustula stingless bees using an active biomonitoring approach. This study demonstrated a pronounced effect of anthropogenic activities on plant anatomy and morphology (higher leaf area, fresh mass, dry mass, and water content in the urban-industrial site), with higher metal concentrations in leaf particulate matter (3.14 ± 0.4 μg cm−2). The diversity of lichens was the lowest, whereas that of crustose lichens was the highest in industrial-urban and residential-rural sites (industrial-urban site = 13 species, residential-rural site = 29 species, control site = 33 species, p < 0.05). The distribution of species within the lichen communities was inversely correlated with the degree of anthropogenic influence. Some lichen species were found exclusively in the control areas, suggesting that they may indicate good environmental quality (Arthonia sp., Astrothelium sp., Phyllopsora pyxinoides, Phyllopsis sp., and others). Beehive pollen analysis revealed the presence of Zn, Cr, Ni, Cu, and Pb, and industrial-urban site exhibited higher metal concentrations (particularly, Ni, 12.59 ± 0.9, and Cr, 3.76 ± 1.00, mg kg−1). This approach highlights the environmental repercussions that affect the Plantae, Fungi, and Animalia kingdoms. The use of biomonitoring as a robust tool in good environmental quality assessment provides insight into policy decisions and underscores the importance of pollution studies.