Despite the United Nations 2030 agenda, large number of both urban and rural dwellers in low-income countries continue to lack access to improved water. Thus, increased effort is required towards enhancing low-cost drinking water treatment technologies especially for developing countries. Slow sand filter (SSF) is one of the most commonly used low-cost and efficient technologies for treating household drinking water. However, effectiveness of SSF is substantially affected by very high turbidity and relatively large amounts of dissolved heavy metals. To enhance removal of both turbidity and heavy metals, this study optimized sand bed depth (SBD) of SSF and investigated the potential of natural zeolite from Uganda for removal of lead, arsenite (As(III)) and fluoride ions from water. To remove lead ions, the zeolite was used in its natural form. However, to remove As(III) and fluoride, the natural zeolite was modified using hexadecyltrimethylammonium bromide solution. Removal of high turbidity was found to require a large optimal SBD. Furthermore, efficiency of treating synthetic turbid water increased with increasing initial turbidity. Variation of final turbidity with SBD was found to be best described by an exponential function. Optimal SBDs on top of an underdrain gravel layer of 0.2 m were 453, 522, 561, and 580 mm for turbidity of 60, 80, 100, and 120 NTU, respectively. Optimized SBD used achieve at least 95% efficiency in removing suspended particles from water with turbidity 120 NTU was found to save up to 35% of the total cost for acquiring sand volume required by a conventional SSF. For a particular zeolite mass, removal efficiencies of lead, As(III) and fluoride generally increased with increasing contact time. Removal efficiencies of lead, As(III), and fluorides were also shown to increase with increasing zeolite mass. Lead removal efficiencies using natural zeolite were 75 and 98% under 20 and 40 min, respectively. Removal of As(III) using modified zeolite mass was 91% within contact time of 10 min. Adsorption of fluoride on modified zeolite was 80% within 5 min. Adsorption of lead, As(III), and fluorides indicated promising potential of natural zeolites from Uganda for treating polluted water.