This paper describes the control of the nucleation and growth of calcite crystals by a matrix composed of an agarose hydrogel on top of a carboxylate-terminated self-assembled monolayer (SAM). The design of this matrix is based upon examples from biomineralization in which hydrogels are coupled with functionalized, organic surfaces to control, simultaneously, crystal morphology and orientation. In the synthetic system, calcite crystals nucleate from the (012) plane (the same plane that is observed in solution growth). The aspect ratio (length/width) of the crystals decreases from 2.1 ± 0.22 in solution to 1.2 ± 0.04 in a 3 w/v % agarose gel. One possible explanation for the change in morphology is the incorporation of gel fibers inside of the crystals during the growth process. Etching of the gel-grown crystals with deionized water reveals an interpenetrating network of gel fibers and crystalline material. This work begins to provide insight into why organisms use hydrogels to control the growth of crystals.