Polychlorinated pesticides (PPs) were classified as persistent organic pollutants because of their toxicity, limited degradability in the environment, bioaugmentation, and accumulation in animal tissues. PPs accumulate in the environment mainly in the soils and water sediments where they are toxic to the decomposer organisms including soil bacteria and fungi. Therefore, there is an urgent need to search for the microorganisms capable of PP biodegradation which could be applied for soil bioremediation. The exact mechanism of PP microbial toxicity is unknown; however, there is evidence that it can be membrane related. To shed light on the interactions of PPs with microbial membranes, we applied Langmuir monolayers formed by phospholipids as model biomembranes. The model membranes were formed by phospholipids typical to microbial membranes: cardiolipins and phosphatidylglycerols the main components of Gram positive bacteria membranes, phosphatidylcholine typical to fungal membranes, as well as phosphatidylethanolamine found in the inner membranes of Gram negative bacteria. For the studies, the most ecotoxic PPs and their water-soluble metabolites were chosen. The monolayers were studied with the application of mutually complementary techniques: Langmuir technique, grazing incidence X-ray diffraction, and PM-IRRAS spectroscopy. It turned out that the cyclodiene PPs are more membrane active than monocyclic PPs and that the possibility of their incorporation is strictly related to the phospholipid structure. The membranes prepared with cardiolipin turned out to be especially resistant to PP incorporation. Regarding the metabolites, pentachlorophenol turned out to be especially structure breaking, affecting the molecular organization of all of the investigated phospholipids.