Despite having approximately 100,000 lakes, Sweden has limited continuous gauged lake water level data. Although satellite radar altimetry (RA) has emerged as a popular alternative to measure water levels in inland water bodies, it has not yet been used to understand the large-scale changes in Swedish lakes. Here, we quantify the changes in water levels in 144 lakes using RA data and in situ gauged measurements to examine the effects of flow regulation and hydroclimatic variability. We use data from several RA missions, including ERS-2, ENVISAT, JASON-1,2,3, SARAL, and Sentinel-3A/B. We found that during 1995–2022, around 52% of the lakes exhibited an increasing trend and 43% a decreasing trend. Most lakes exhibiting an increasing trend were in the north of Sweden, while most lakes showing a decreasing trend were in the south. Regarding the potential effects of regulation, we found that unregulated lakes had smaller trends in water level and dynamic storage than regulated ones. While the seasonal patterns of water levels in the lakes in the north are similar in regulated and unregulated lakes, in the south, they differ substantially. This study highlights the need to continuously monitor lake water levels for adaptation strategies in the face of climate change and understand the downstream effects of water regulatory schemes.