This study proposes a methodology for deriving boundary conditions in the presence of boundary layers by using integral conjugation conditions for thin geobarriers. These boundary conditions are essential part of the boundary value problems such as mathematical models of physical, chemical and hydrological processes. The developed approach allows to account for variable characteristics of the boundary layer material. Such consideration is significant in mathematical and computer modelling of environmental processes with strong nonlinear effects. By applying the proposed methodology, we derive balance boundary conditions for: soil surface moisture and temperature in case the soil is covered with growing crops or a layer of fallen leaves; salt concentration in pore water under carst processes; greenhouse gas distribution on the soil-atmosphere contact in the presence of growing plants.