This paper describes an experimental characterization scheme of the biophysical properties of reconstituted hydrogel matrices based on indentation testing, quantification of transport via microfluidics, and confocal reflectance microscopy analysis. While methods for characterizing hydrogels exist and are widely used, they often do not measure diffusive and convective transport concurrently, determine the relationship between microstructure and transport efficiency, and decouple matrix mechanics and transport properties. Our integrated approach enabled independent and quantitative measurements of the structural, mechanical, and transport properties of hydrogels in a single study. We used fibrillar type I collagen as the base matrix and investigated the effects of two different matrix modifications: 1) cross-linking with human recombinant tissue transglutaminase II (hrTGII) and 2) supplementation with the non-fibrillar matrix constituent hyaluronic acid (HA). hrTGII modified matrix structure and transport but not mechanical parameters. Furthermore, changes in matrix structure due to hrTGII were seen to be dependent on the concentration of collagen. In contrast, supplementation of HA at different collagen concentrations altered matrix microstructure and mechanical indentation behavior but not transport parameters. These experimental observations reveal the important relationship between ECM composition and biophysical properties. The integrated techniques are versatile, robust, and accessible; and as matrix-cell interactions are instrumental for many biological processes, the methods and findings described here should be broadly applicable for characterizing hydrogel materials used for 3-D tissue engineered culture models.