The Mar Menor is the second largest coastal lagoon in the Mediterranean Sea with a surface area of about 136 km2. It is restricted from the open sea by a sandy barrier system (La Manga) interrupted by three tidal inlets. As a result of high evaporation it is hypersaline (42-47 ppt) in parts. This study examines the factors leading to the rise in sea surface temperature in the Mar Menor through the analysis of long-term sea surface temperature using HadSST1.1 data together with shorter term MODIS and OISST data. A thermal box model has been constructed for the lagoon in an attempt to balance major heat sources and sinks. As well, a thermal probe was deployed in 0.3 m of water to evaluate the benthic flux of heat of the shelly fine sand that covers the lagoon seabed. Results show that the vertical thermal gradient in the seabed inverts between the day and night. Prior to 1980 there was no clear trend in SST and variations were strongly associated with the AMO and NAO. Post 1980, maximum summertime SST showed a steady increase of 0.34°C/decade. Cross-correlation of SST in the Mar Menor with external drivers showed that it is dominated by SST of the Western Mediterranean, followed by CO2, AMO and IOD. There was a strong inverse relationship with sun spot activity and the Spanish national GDP. There were no significant links in trends between SST in the Mar Menor and PDO, NAO or ENSO3,4 in a Spearman Rank order evaluation and PCA analysis.