This paper physically and numerically models the influence of biofilms on heavy metal removal in a gravel filter. Experimental flow columns were constructed to determine the removal of Cu, Pb and Zn by gabbro and dolomite gravel lithologies with and without natural biofilm from sustainable urban drainage systems (SuDS). Breakthrough experiments showed that, whilst abiotic gravel filters removed up to 51% of metals, those with biofilms enhanced heavy metal removal by up to a further 29%, with Cu removal illustrating the greatest response to biofilm growth. An advection–diffusion equation successfully modelled metal tracer transport within biofilm columns. This model yielded a permanent loss term (k) for metal tracers of between 0.01 and 1.05, correlating well with measured data from breakthrough experiments. Additional 16S rRNA clone library analysis of the biofilm indicated strong sensitivity of bacterial community composition to the lithology of the filter medium, with gabbro filters displaying Proteobacteria dominance (54%) and dolomite columns showing Cyanobacteria dominance (47%).