Faecal contamination of surface waters is a global public health and economic burden. Here, we constructed a 30-year dataset to analyse the spatiotemporal trends and driving mechanisms of faecal coliforms (FCs) in China. We found that previous national policies to reduce water pollution have significantly improved the quality of surface water and, correspondingly, faecal contamination. However, the downward trend in FC levels has been more gradual than that for physico-chemical pollutants, and this trend may be exaggerated. Our results show that the driving mechanisms of faecal pollution were seasonal and complex. During the dry season, forests and grasslands were the source landscapes that exacerbated faecal pollution; during the wet season, urbanisation dominated, highlighting China's poorly designed drainage systems. Our projections revealed that faecal contamination will continue to worsen from 2022 to 2035, highlighting the need for pollution control. In the future, faecal indicators should be included in routine monitoring, evaluation, and assessment at the national level. Moreover, coordinated design of forest, grassland, and wetland landscapes is recommended for faecal pollution control at the regional level, whereas stormwater-related source control needs to be further strengthened at the urban level.