Of the world's liquid freshwater resources, 97% is stored as groundwater. For millennia, humans have used this resource to provide water for domestic use, agriculture and industry. The water quality of groundwater for drinking water, specifically, is important to human health and therefore the health of society. The focus of this doctoral thesis is on the microbial water quality of groundwater intended for drinking water consumption. The presence and transport of pathogenic microorganisms in the subsurface is difficult to detect and quantify due to their low concentrations in the environment. It is possible to perform field tests by injecting high concentrations of a colloidal tracer and taking measurements along the groundwater flow path; however, to ensure groundwater protection, it is not allowed to inject real pathogenic microorganisms. Surrogates that are representative of the microorganisms under consideration need to be developed. The aim of this doctoral thesis is twofold: to study microbial transport in the subsurface by developing surrogates for two common and persistent pathogenic microorganisms, Cryptosporidium parvum and human adenovirus, and to use an appropriate method for detection and quantification of low concentrations of microorganisms and surrogates in environmental water. Following the Introduction, Chapter 2 addresses the problem of detecting low concentrations of colloids in groundwater, as compared to surface water and a control of sterile deionized water. It was found that surrogates could be detected in very turbid lake water down to a size of 0.75 -m and a maximum sample volume of 1 ml. In pristine spring water, colloids could be quantified down to a size of 0.5 -m in a maximum volume of 500 ml. Chapter 3 goes on to use the method developed in Chapter 2 to enumerate low concentrations of surrogates representing C. parvum in laboratory column tests with granular limestone aquifer material. The best surrogate for C. parvum, as indicated by parameters calculated using colloid filtration theory and breakthrough curves, was a glycoprotein-coated microsphere. Surrogates representing human adenovirus were compared in Chapter 4 in order to determine the most ideal surrogate of those tested and the removal mechanism in limestone material. PRD1 phage was found to be the surrogate best representing human adenovirus removal in high carbonate material, but failed to mimic the detachment of human adenovirus under high ionic strength and high pH conditions. In this doctoral thesis, two strategies were developed to further advance colloid tracer technology and the enumeration of colloids. The implication of this work is that each system comprising of aquifer media, certain chemical conditions and a specific microorganism is unique and needs to be considered on a case by case basis. Due to the complexity of the system, microbial transport in one material cannot be generalized to represent transport in all groundwater systems. This makes it almost impossible to establish standard methods to monitor drinking water quality in the subsurface. In conclusion, experimental field tests using a surrogate that is compared to the pathogenic microorganism in laboratory tests is recommended. With the results obtained from such tests, the transport processes of pathogenic microorganisms in groundwater can be better characterized and this would enable a risk approach analysis to be used.