Hydrostructural parameters are driven by the characterization of the soil aggregates structure using a set of thermodynamic equations. Soil aggregates structure is unique for each soil type and can be affected by its physical, chemical, and biological properties. Because it so completely represents those properties, tracking the changes in soil aggregates structure can be used to develop quantitative indicators of soil quality. This study involves a field experiment to examine pedostructure-based soil characterization under different soil management practices. It investigates the feasibility of defining a new soil quality indicator. Three organic amendments (chicken manure, dairy manure, and milorganite) were applied at 0, 168, 336, 672 kgN/ha (rate 0, 1, 2, and 3) for 36 plots of 3 m. × 1.5 m. After extracting 12 hydro-structural parameters from TypoSoil™ measurements, statistical analysis was used to evaluate the sensitivity of these parameters to management practices. Results showed that increasing the application rate from 1 to 3 showed no significant effect on hydrostructural parameters for all treatments. However, treatments significantly enhanced water content and available water in the A horizon. In the B horizon, only rate 3 affected available water for chicken and dairy manure. Comparing the three treatments, dairy manure’s significance was prominent and promising for improving soil aggregates structure in rates greater than 1. The best application rate to improve soil aggregates structure for chicken manure seems to be 1, for dairy manure rate 2, and milorganite rate 3.