The paper presents the results of the analysis of diatoms from surface sediments (stones, sands) and macroflora (seagrass, macroalgae) collected at 16 sampling sites located along the inner coastal zone of Puck Bay (southern Baltic Sea) along the Hel Peninsula. The main diatom species of epilithon, epipsammon and epiphyton were characterized with respect to their autecological preferences (habitat, salinity, trophic status, saprobity). Three groups of diatoms were distinguished with respect to the type of substrate based on the results of benthic flora analysis: diatoms (i) of one type of substrate, (ii) of two types and (iii) those occurring on all types of substrates. Moreover, the distribution of benthic diatom communities indicates ecological differences in the study area. Marine and brackish-water species were observed in large numbers in the coastal zone of the Outer Puck Bay, whereas freshwater flora occurred with a higher frequency in the coastal zone of the Puck Lagoon. The content of polysaprobionts and of α-mesosaprobionts indicates that the region of the Hel Tip is highly eutrophicated and very polluted. The coast in the vicinity of Kuznica is less polluted, whereas the best environmental conditions are found in the Jurata–Jastarnia region, as evidenced by the frequency of diatoms that are β-mesosaprobionts.