We examined the performance of two household water treatment and safe storage (HWTS) systems, the Danvor plastic biosand filter and the Potters for Peace Filtron ceramic filter, under ideal as well as modified operating conditions using systematic and comparable measurements. The operating variables for the biosand filter were (i) pause times between filtration runs, (ii) water-dosing volumes and (iii) the effluent volume at which a filtered water sample was collected. For the ceramic filter we examined overflow filtration versus standard filtration. We used the bacterial indicators of total coliforms and Escherichia coli to quantify microbiological removal. With the biosand filter, a 12 h pause time had significantly higher total coliform removal than a 36 h pause time at the 20 l collection point (79.1% versus 73.7%; p < 0.01) and borderline significance at the 10 l collection point (81.0% versus 78.3%; p = 0.07). High-volume filtration (20 l) had significantly lower total coliform removal efficacy than low-volume (10 l) filtration at the 10 l collection point (81.0% versus 84.2%; p = 0.03). We observed a decreasing trend in total coliform removal by sample collection volume with the highest removal efficacy at the 5 l sample collection point (versus at the 10 and 20 l collection points). Using the ceramic filter, mean total coliform and E. coli removal were significantly lower (p < 0.01) in overflow filtration than in standard filtration. The findings indicate that operating conditions can reduce the effectiveness of the systems in a field-based setting and increase environmental risk exposure.