In this Ph.D. thesis, I investigated the mechanics of soft matter, specifically focusing on the viscoelastic-plastic response of agarose and fibrin networks. The study utilized a combination of experimental observations, statistically based continuum mechanics, and discrete numerical modeling techniques to develop physically based computational models of biological soft materials. In Chapter 2, I proposed a novel model for predicting the time-dependent behavior of agarose networks which offered insights into bond kinetics that can be applied to other biopolymer networks. Chapter 3 presented a coarse-grained, discrete numerical model for examining topological changes in transient semi-flexible networks, capturing the appropriate physics for various temperature limits and deformation rates. In Chapter 4, I concentrated on fibrin gels. I developed two models to better understand their behavior. The first, a comprehensive protofibril bundle model, was designed to capture the energetic penalty linked with highly stretched networks. The second, a fibrin fiber model, aimed to capture the macroscopic viscoelastic response of the gels and predict network realignment following applied deformation. This research has broad implications for biopolymer networks, bioengineering, tissue engineering, and cell-scale mechanobiology. By characterizing the critical microstructural features and dynamics that dictate the mechanical response of semi-flexible networks, I lay the foundation for further advancements in material choice, design, and the understanding of the interplay between soft matter physics and biological processes.