Elevated faecal pollution of water bodies poses public health risks for humans as well as livestock, and degrades aquatic ecosystems. This paper presents levels, patterns and sources of faecal pollution detected in a yearlong investigation of the River Njoro watershed, a crucial source of surface and ground water for communities and ecosystems in and surrounding the watershed, including Nakuru Municipality and Lake Nakuru. Under the SUMAWA Project, an extensive survey was conducted of the stream network and numerous point and non-point sources of faecal pollution. Then faecal coliform levels were monitored monthly throughout the River Njoro main stream and Little Shuru tributaly. New gene-based detection methods were tested to distinguish cow from human sources of faecal contamination, and test for markers of Cryptosporidium spp., a water-borne pathogen known to cause severe diarrhoea in very young, old, and immuno-compromised humans and cattle. High levels of faecal water pollution were measured throughout the watershed, averaging 8,000 colony forming units (cfu) of faecal coliform per l00 ml of river water over the year. Periods and incidents exceeding 100,000 cfu/100 ml occurred at l0 out of l5 monitored locations, at some places during the dry season, and nearly everywhere during high runoff months of August and/or July. A pattern of faecal pollution peaking in August at all sites, signiﬁcantly higher levels detected when cattle were present watering at a site, and the widespread detection of cow genetic source faecal markers, point to livestock, in particular cattle, as the dominant and most widespread likely cause of gross faecal pollution and a possible source of Cryptosporidiunz spp. in the River Njoro Watershed. Detailed ﬁndings are presented and actions explored to control identiﬁed sources and reduce high pollution levels and their damaging impacts on local ecosystems, livelihoods, and public health.