In Earth's aquatic environments and the human body, microbial swimmers often accumulate at interfaces within layered systems, forming colonies known as active carpets. These bioactive layers enhance mass transport and diffusion in fluid media. Here we study the hydrodynamic behavior induced by active carpets within confined semi-infinite fluid layers, such as the one found in the sea surface microlayer. By deriving analytical expressions and performing numerical simulations, we explore how geometrical and viscous confinement (layer thickness and viscosity ratio) influence hydrodynamic fluctuations and passive tracer dynamics. Our findings reveal anisotropic distributions of fluctuations, characterized by three distinct regions: near the active carpet and fluid-fluid interface (Region I), vertical fluctuations dominate; in an intermediate region (Region II), fluctuations become isotropic; and near the free surface (Region III), horizontal fluctuations prevail. The results also demonstrate the emergence of coherent vortical structures in highly confined systems, with roll-like patterns governed by the thickness of the confined layer and the sharpness in viscosity transitions. The insights provided by this work have implications for understanding biogenic flow patterns and transport processes in natural and engineered environments, offering potential applications in areas such as microbial ecology, biofilm management, and microfluidic technologies.