A new sensor for in situ, real time methane (CH4) measurements in aqueous environments is based on the refractive index (RI) modulation of a sensitive film composed of a polydimethylsiloxane (PDMS) layer incorporating molecules of cryptophane-A. The RI varies according to the amount of CH4 bound to the cryptophane-A in the film and is determined using surface plasmon resonance (SPR). Tests of the sensor in the summer of 2012 reveal the expansive range of conditions of the Central Baltic Sea with CH4 concentrations varying from 5 nM up to a few hundred nanomolar. The sensor showed detection limits down to 3 nM, sensitivity of 6 to 7 × 10(-6) RIU/nM, and response times of 1 to 2 min. Best responses were obtained for concentrations up to 200 nM. Side effects (temperature, cross-sensitivity) are reviewed for future improvements to the sensor design. CH4 values are highest in the Landsort Deep up to 1.2 μM at 400 m depth and lowest in the Gotland Deep with 900 nM at 220 m depth. However, variable values in the upper layers indicate higher mixing rates due to currents and wind driven forces in the Gotland Basin compared with almost constant CH4 values in the Landsort Deep.