Substrate reactors used to treat water have generally been vertical, and many settling ponds have zigzag baffles to increase the actual residence time. To improve the shape and flow configurations, baffle-type, weir-type, column-type, and SAPS-type reactors and settling ponds with zigzag and hanging baffles were studied by bench-scale and pilot-scale experiments and theoretical considerations. Tracer tests indicated that the extension of the flow line by zigzag baffles could prevent the short-circuiting of the SAPS-type reactor. The pilot-scale reactor with baffles in the longitudinal direction exhibited the highest treatment efficiencies among the baffle-type, weir-type, and column-type reactors. Nevertheless, the required hydraulic head is a critical constraint in the application of various types of reactors. The relationship between the maximum flow rate and the difference in hydraulic head or hydraulic conductivity indicated applicable flow rates for the baffle-type and weir-type reactors. If the hydraulic head difference is sufficiently high by pumping or the flow rate is sufficiently low, application of zigzag baffles in the longitudinal direction is highly encouraged in substrate reactors. Furthermore, pilot-scale experiments with a settling pond with zigzag baffles and hanging baffles indicated that the prevention of surface flow by using the hanging baffles reduced the required residence times to 51 %–69 % of those of zigzag baffles. The increased efficiency of the suggested reactors and settling ponds will decrease the required area and cost of construction.