Lake Łebsko is the largest and most productive coastal lake of the southern Baltic Sea to which it is permanently connected. The shoreline is well-developed, and the lake is divided into three parts: eastern, central, and western. Seawater intrusion affects most strongly the eastern part, where the Łeba River connects it with the sea. Samples of water and sediments were collected in 2014–2015. In the same places and time interval, bottom fauna was collected to determine the influence of environmental predictors on its qualitative-quantitative structure. Metals Cr (chromium), Pb (lead), Ni (nickel), Cu (copper), and Al (aluminium) in the samples were analyzed using inductively coupled plasma optical emission spectrometry. Most of the analyzed physicochemical variables of water were significantly higher in the eastern part: conductivity, salinity, sulfates (p < 0.0001) and chlorides (p = 0.01). Metal concentrations in water did not differ significantly between the lake parts, but in sediments they were generally higher in the western part. During the study, we detected significant changes in descriptors and abundance of the major groups of benthic fauna (Oligochaeta and Diptera), mostly between the eastern and western parts. BIO-ENV analysis showed that the benthic community of Lake Łebsko is shaped primarily by physicochemical variables of water (42% of the variance), linked with intrusion of seawater. Secondarily, the structure of the benthic community is affected by the amounts of heavy metals in sediments (31%) and water (12%). The findings can help us improve the principles of management of coastal lakes, including modification of hydrological conditions.