Extreme weather events, such as heavy rainfall, are being increased by climate change in various regions, and such events often cause floods. This study examined the trends and variability of extreme rainfall indices using daily rainfall data (1981–2023) from three study sites at different socio-economic development spectra in Vhembe District, Limpopo Province, South Africa. The analyses focus on indices such as the annual total rainfall from wet days (PRCPTOT), the maximum number of consecutive dry days (CDD) and wet days (CWD), annual maximum 1-day and 5-day rainfall (RX1 day and RX5 day), the Simple Daily Intensity Index (SDII), the number of days exceeding varying amounts of precipitation (R10, R20, R40) and the annual number of wet days with rainfall greater than the 95th and 99th percentile (R95p and R99p) of the 1981–2023 daily rainfall. We discuss the observed trends in extreme rainfall indices in light of the actual flood occurrences to establish linkages. Several statistically significant and marginal changes in extreme rainfall trends were identified and provided key insights into reported flooding events in the district—flooding episodes were mainly attributed to the significant increases in total precipitation (PRCPTOT) and rainfall exceeding the 99th percentile of daily rainfall (R99p). Other significant contributors were declining CDD and increasing RX1day at Duthuni, increasing R40 at Musina as well as increasing R1 and declining CDD at Sane. However, the low altitude, urbanization, poor waste management and inadequate drainage systems were among the key non-climatic drivers of flood risk across the study sites, but these warrant further investigation. The complex interplay between climatic and non-climatic drivers of flood risk underscores the importance of localized climate studies and the need for adaptive strategies to minimize loss and damage. Overall, this research provides valuable insights into localized extreme rainfall trends, which are essential for developing site-specific flood mitigation and adaptation strategies. However, such initiatives require placing vulnerable communities at the centre in order to develop solutions that are locally led and relevant.