Marine heatwaves (MHWs) are known to pose a threat to aquatic ecosystems and coastal communities and, as a result, they receive significant attention nowadays, thus motivating our scientific interest in better understanding the regional patterns of these events. In this study, we analyze MHWs in the SE part of the Baltic Sea, defining them as anomalously warm water events, where the water temperature exceeds the 90th percentile threshold of the corresponding calendar day for at least five or more consecutive days. Our study is based on a combination of long-term (1993–2023) in situ data, field measurements, and satellite-derived sea surface temperature data during the warm (May–August) period. Study results suggest that although short-lived (5–9 days) MHW events typically dominate throughout the analyzed period, the occurrences of longer (more than three weeks) and more intense MHWs have increased in our study region in the recent decade. The heatwaves are observed both in coastal and open waters, with SST anomalies up to around 5–6 °C above the 90th percentile threshold during extreme events, extending thermal influence as deep as 20 m during prolonged and more intense events. We believe that the results of this study contribute to a better understanding of MHW patterns in the study region, which is important from an ecological and socio-economic point of view, providing valuable insights for human health aspects as well.