Column experiments are often used to study transport properties of sediments to predict the fate of contaminants in the subsurface. However, water flow in column experiments is rarely monitored over the entire length of experiments, despite the known impact of biogeochemical processes on pore structures. To study if flow path changes occur over time, water flow and solute transport were investigated in a homogeneous, nearly saturated column by conducting three tracer experiments over 7 mo. Water flow and transport parameters were determined from tracer breakthrough curves using different model approaches. The initial homogeneous transport was adequately described by a simple advection-dispersion model. However, after some months, the porous medium changed from being uniform to non-uniform. The observed bimodal breakthrough curves were simulated with a simple multi-flow advection-dispersion and a dual-permeability model. Both models supported the development of non-uniform water flow and solute transport due to flow paths changes. Those changes were attributed to clogging of small pores near the column inlet due to microbial growth and calcite precipitation leading to a heterogeneous infiltration front. The results highlight the need to determine transport properties continuously over the course of column experiments to reliably predict parameters for groundwater flow and understand contaminant transport into aquifers.