Gravel aquifers act as important potable water sources in central western Europe, yet they are subject to numerous contamination pressures. Compositional and textural heterogeneity makes protection zone delineation around groundwater supplies in these units challenging; artificial tracer testing aids characterization. This paper reappraises previous tracer test results in light of new geological and microbiological data. Comparative passive gradient testing, using a fluorescent solute (Uranine), virus (H40/1 bacteriophage), and comparably sized bacterial tracers Escherichia coli and Pseudomonas putida, was used to investigate a calcareous gravel aquifer’s ability to remove microbiological contaminants at a test site near Munich, Germany. Test results revealed E. coli relative recoveries could exceed those of H40/1 at monitoring wells, 10 m and 20 m from an injection well, by almost four times; P. putida recoveries varied by a factor of up to three between wells. Application of filtration theory suggested greater attenuation of H40/1 relative to similarly charged E. coli occurred due to differences in microorganism size, while estimated collision efficiencies appeared comparable. By contrast, more positively charged P. putida experienced greater attenuation at one monitoring point, while lower attenuation rates at the second location indicated the influence of geochemical heterogeneity. Test findings proved consistent with observations from nearby fresh outcrops that suggested thin open framework gravel beds dominated mass transport in the aquifer, while discrete intervals containing stained clasts reflect localized geochemical heterogeneity. Study results highlight the utility of reconciling outcrop observations with artificial tracer test responses, using microbiological tracers with well-defined properties, to characterize aquifer heterogeneity.