<p>Dataset used in the analysis.</p>

Low-income urban areas experience challenges in accessing safe water due to poor infrastructure and illegal connections, leading to microbial contamination and worsening health risks. This study investigates the association of household water handling practices with microbial drinking water quality in Kibera – the largest urban informal settlement in Nairobi, Kenya. We conducted a cross-sectional study in December 2022 in Kibera with 262 randomly selected households to assess water handling practices, and physicochemical and microbial water quality. Most households (84%) had Free Chlorine Residual (FCR) below the recommended levels (≥ 0.2 mg/L) indicating insufficient protection against microbial contamination. Water samples from 56% and 15% of households tested positive for total coliforms and E. coli respectively. Only 42% of households treated their drinking water at home. Multivariate logistic regression revealed significantly higher odds (AOR = 3.16, p < 0.001) of contaminated drinking water (E. coli or total coliforms) amongst households not treating water. Those maintaining recommended FCR levels had substantially lower odds (AOR = 0.04, p < 0.001) of microbial contamination. In a bivariate sub-analysis, chlorine-based water treatment methods were protective against microbial contamination (OR=0.26, p = 0.025). In contrast, filtration-based methods were linked to higher odds of contamination (OR=3.25, p = 0.008) and boiling had no effect (p = 0.671). This study underscores the need for public health actors to promote effective and sustained water handling practices, especially for settings at high risk of contamination such as low-income urban areas.