In rural Ecuador, microbial water contamination is associated with child morbidity mainly due to gastroenteritis. Black ceramic water filters (BCWF) are a new household water treatment recently developed to improve microbial removal from the classical model implemented worldwide. This study has assessed BCWF microbial performance at laboratory level by continuous filtering of spiked water with microbial surrogates (Escherichia coli and MS2 bacteriophage) and highly contaminated surface water to evaluate physicochemical pollutants' removal. At field level, baseline studies in Nanegal and Gualea districts have been performed to evaluate water quality and hygiene practices among communities and a six-month BCWF field implementation study in the Santa Marianita community. Results revealed poor drinking water quality in communities studied. Water treatment practices at household level were reported in low percentages. Conversely, results in BCWF filter assays at laboratory level for 600 litres of usage have shown 5.36 logarithms of bacterial removal and 3.83 logarithms for viral removal and significant reductions of physicochemical pollutants considering international standards. BCWF implementation in the Santa Marianita community reveals promising results on microbial water quality in households using this new technology. However, it is important to reinforce correct BCWF maintenance for better performance at field level.