An overlooked source of faecal contamination of rivers comes from misconnected pipes from residential properties. With a large increase in housing developments along with property extensions, there is widespread concern that piping networks are not being adequately checked for misconnections before property sales. Two surveys of 45 sites on the River Lee and its tributaries used coliforms and biofilm communities to identify misconnection hotspots, with the focus on contamination from raw sewage. Between the 2013 survey and a repeat in 2020, there has been a significant increase in the number of coliforms from surface water outfalls from an average of 43,693 cfu per 100ml to 123,797 cfu - nearly a three-fold increase. The percentage of misconnections containing raw sewage was calculated as 7.2% in 2014, increasing to 10.6% in 2020, thus suggesting an increase in the number of misconnections. The biofilm communities that developed on tiles pegged into the river substrate below surface water outfalls were categorised by three community groupings: clean communities, a transitional group and dirty communities. A clear separation between these groups can be seen in the DECORANA plots. CCA found a relationship between taxa in clean and dirty sites associated with coliform counts. This study highlights that the contribution of raw sewage is underestimated, and this is becoming a persistent and serious pollution problem, especially in urban rivers where the increase is greater. Using coliform testing and biofilm communities in combination will highlight misconnection hotspots.