As a typical waterway modification, the spur dike narrows the water cross section, which increases the flow velocity and flushes the riverbed. Meanwhile, it also protects ecological diversity and improves river habitat. Different types of spur dikes could greatly impact the interaction between flow structure and local geomorphology, which in turn affects the evolution of river aquatic habitats. Four different types of spur dikes—including rock-fill, permeable, w-shaped rock-fill, and w-shaped permeable—were evaluated using flume experiments for spur dike hydrodynamics and fish aggregation effects. Based on Shannon’s entropy, an index for calculating water flow diversity is proposed. Additionally, the impact of the different spur dikes on water flow diversity and the relationship between water flow diversity and fish aggregation effects were studied. The water flow diversity index around the spur dike varied from 1.13 to 2.96. The average aggregation rate of test fish around the spur dike was 5% to 28%, and the attraction effect increased with increasing water flow diversity. Furthermore, we plotted the relationship between water flow diversity index and average fish aggregation rate. A fish hydroacoustic study conducted on the Laohutan fish-bone dike in the Dongliu reach of downstream Yangtze River showed that the fish aggregation effect of the permeable spur dike was greater than the rock-fill spur dike. These research results could provide theoretical support for habitat heterogeneity research and ecologically optimal design of spur dikes.