Field observations provided the basis for a numerical model designed to quantify the vertical mass flux of material initially injected at the base of the water column in a small lake; a process called sub-aqueous disposal. Eddy diffusion estimation largely controlled the transport behaviour, highlighting the need for measurements of diffusion in deep strongly stratified environments. The model followed the contaminant development over 40 years and showed that (i) it is unlikely that any material can ever be completely disposed of over realistic scales and (ii) within the bounds limited by uncertainty in eddy diffusivity, turnover penetration and surface layer precipitation-driven flushing are the mechanisms most likely to have bearing on the contaminant distribution.