This paper presents results of chemical and bacteriological examinations of surface and subsurface water layers of estuarine lake Gardno. The obtained data indicate that there are substantial differences in chemical compound concentrations and also bacteria number and activity between the water layers under investigation. Particularly great differences between microlayers and subsurface water refer to concentrations of organic phosphorus and nitrogen. It was found that bacteria number was greater in surface water layers than in subsurface water. Significant differences among the studied chemical and bacteriological parameters were revealed between particular sites across lake Gardno. The number of freshwater, brackish and marine bacteria in the water of lake Gardno was up to chlorides concentration.