Longitudinal in vivo monitoring is essential for the design and evaluation of biomaterials. An ideal method would provide three-dimensional quantitative information, high spatial resolution, deep tissue penetration, and contrast between tissue and material structures. Photoacoustic (PA) or optoacoustic imaging is a hybrid technique that allows three-dimensional imaging with high spatial resolution. In addition, photoacoustic imaging allows for imaging of vascularization based on the intrinsic contrast of hemoglobin. In this study, we investigated photoacoustic computed tomography (PACT) as a tool for longitudinal monitoring of an implanted hydrogel in a small animal model. Hydrogels were loaded with gold nanorods to enhance contrast and imaged weekly for 8 weeks. PACT allowed non-invasive three-dimensional, quantitative imaging of the hydrogels over the entire 8 weeks. Quantitative volume analysis was used to evaluate the in vivo degradation kinetics of the implants which deviated slightly from in vitro predictions. Multispectral imaging allowed for the simultaneous analysis of hydrogel degradation and local vascularization. These results provide support for the substantial potential of PACT as a tool for insight into biomaterial performance in vivo.