Onsite wastewater systems, widely used in the United States and abroad, often rely on infiltration of effluents into native soils for tertiary treatment and natural disinfection. The processes that govern soil clogging and hydraulic performance during infiltration into soil are complex and involve a dynamic interaction between physical, chemical, and biological processes. The authors link the development of soil clogging in onsite systems with the fundamental physical, chemical, and microbial processes that can occur during wastewater reclamation in soil environments. They provide a critical review of onsite wastewater systems, outlining the different types of wastewater-induced soil clogging, clogging locations, and clogging materials. The authors then focus on the influence of oxygen concentration on clogging and the environmental conditions that stimulate the accumulation of organic materials from microbial metabolism. Correlations are made between observational data in porous media studies and microbial metabolism. The objective of this review is to increase understanding of the processes that govern hydraulic performance of onsite wastewater systems during effluent infiltration and potentially improve system design and operation.