In this paper we describe the seasonal characteristics of the vertical thermohaline structure of the shallow waters of the southeastern part of the Baltic Sea off the Kaliningrad region using the field data of research cruises. The analysis of the original set of experimental data in 2003–2014 confirmed that heating and cooling processes occur, as a rule, at a depth of 30–35 m. The upper 5–10 m layer of water is involved in the heat exchange with the atmosphere. The depth of the thermocline varies from 10–30 m up to 17–35 m in spring and summer. Salinity field of the Baltic shallow water is characterized by a small range of variability in all seasons. Fluctuations in the measured values of salinity in coastal waters do not exceed 0.5 PSU (Practical Salinity Unit). The greatest variations in the salinity of coastal waters (up to 0.7 PSU) are characteristic of the upper layer 5 to 10 m thick in winter and summer. Average seasonal linear trends of temperature and salinity variation were obtained.