A groyne zone formed by installing groynes functions as habitat or shelter for aquatic organisms during a flood. Since flow characteristics over a groyne zone are affected directly by groynes, understanding flow patterns due to shapes and types of groynes is of importance for designing groynes. In order to use groynes as an eco-friendly river structure, the ecological effects should also be considered at the design stage. In Korea, the ecological effects of groynes have rarely been examined or included for the actual design. In this study, a set of experiments were carried out to investigate flow pattern changes depending on different types of groynes. Based on the flow characteristics in the groyne zone, the scales of habitats and shelters by the groyne types were estimated. In addition, to test the applicability of a habitat evaluation model to the ecological design of groynes, River2D was used for a virtual river. For assessment of the groyne’s function of ecological habitat, the suitability index of a habitat for pale chub, one of the popular fishes in Korea, was used and the habitat areas by the groyne types were analyzed. The flow changes depending on the groyne types simulated by River2D show the applicability for the simulation of an ecological habitat to the groyne design.