Recharge of waste water in an unconsolidated poorly sorted alluvial aquifer is a complex process, both physically and hydrochemically. The aim of this paper is to analyse and conceptualise vertical transport mechanisms taking place in an urban area of extensive wastewater infiltration by analysing and combining the water balance, the microbial (Escherichia coli) mass balance, and the mass balance for dissolved solutes. For this, data on sediment characteristics (grain size, organic carbon, reactive iron, and calcite), groundwater levels, and concentrations of E. coli in groundwater and waste water were collected. In the laboratory, data on E. coli decay rate coefficients, and on bacteria retention characteristics of the sediment were collected via column experiments. The results indicated that shallow groundwater, at depths of 50 m below the surface, was contaminated with E. coli concentrations as high as 10⁶ CFU/100 mL. In general, E. coli concentrations decreased only 3 log units from the point of infiltration to shallow groundwater. Concentrations were lower at greater depths in the aquifer. In laboratory columns of disturbed sediments, bacteria removal was 2-5 log units/0.5 cm column sediment. Because of the relatively high E. coli concentrations in the shallow aquifer, transport had likely taken place via a connected network of pores with a diameter large enough to allow bacterial transport instead of via the sediment matrix, which was inaccessible for bacteria, as was clear from the column experiments. The decay rate coefficient was determined from laboratory microcosms to be 0.15 d^{- 1}. Assuming that decay in the aquifer was similar to decay in the laboratory, then the pore water flow velocity between the point of infiltration and shallow groundwater, coinciding with a concentration decrease of 3 log units, was 0.38 m/d, and therefore, transport in this connected network of pores was fast. According to the water balance of the alluvial aquifer, determined from transient groundwater modelling, groundwater flow in the aquifer was mainly in vertical downward direction, and therefore, the mass balance for dissolved solutes was simulated using a 1D transport model of a 200 m column of the Quaternary Alluvium aquifer. The model, constructed with PHREEQC, included dual porosity, and was able to adequately simulate removal of E. coli, cation-exchange, and nitrification. The added value of the use of E. coli in this study was the recognition of relatively fast transport velocities occurring in the aquifer, and the necessity to use the dual porosity concept to investigate vertical transport mechanisms. Therefore, in general and if possible, microbial mass balances should be considered more systematically as an integral part of transport studies.