Sea surface temperature (SST) is a key hydrological variable which can be monitored via satellite. One source of thermal data with a spatial resolution high enough to study sub-mesoscale processes in coastal waters may be the Landsat mission. The Thermal Infrared Sensor on board Landsat 8 collects data in two bands, which allows for the use of the well-known nonlinear split-window formula to estimate SST (NLSST) using top-of-the-atmosphere (TOA) brightness temperature. To calibrate its coefficients a significant number of matchup points are required, representing a wide range of atmospheric conditions. In this study over 1200 granules of satellite data and 12 time series of in situ measurements from buoys and platforms operating in the Baltic Sea over a period of more than 6 years were used to select matchup points, derive NLSST coefficients and evaluate the results. To filter out pixels contaminated by clouds, ice or land influences, the IdePix algorithm was used with Quality Assessment Band and additional test of the adjacent pixels. Various combinations of flags were tested. The results show that the NLSST coefficients derived previously for coastal areas, characterised by a more humid atmosphere, might overestimate low SST values. Formulas derived for the Baltic Sea produced biases close to 0 °C and RMSEs in the range of 0.49–0.52 °C.