The surface water microlayer (SML) is a thin layer found at the interface of the hydrosphere and the atmosphere. It is capable of accumulating chemical substances and microorganisms at a rate as high as 100-fold greater than that observed in the subsurface water. The rate of accumulation of biogens and chlorophyll a in SML of an estuary, where marine and fresh waters mix, varies considerably and it depends on the degree mixing of these waters, which is manifested in the varying values of the enrichment factor (EF, calculated as the ratio of nutrients concentration in SML versus subsurface water). The influence of the Baltic Sea marine water and the freshwater Łeba River inflows on the estuarine Lake Łebsko (Poland) was examined. Nine sampling sites were located in the estuary. Water samples were collected from two layers: the surface microlayer (thickness 242 µm ± 40) and the subsurface water (15 cm depth). The capacity of the SML to enrich the water in nutrients and chlorophyll differed among various parts of the estuary, as well as between seawater and river waters. Statistically significant higher EF were found in the marine waters than in river waters for the nitrogen and phosphorus compounds as well as chlorophyll. There were also differences in EF between marine and lake waters. The highest EF were also recorded for organic forms of nitrogen and phosphorus in marine water. Most probably, marine flux into the estuarine Lake Łebsko, resulted in the increased EF for these investigated components.