We present a novel indentation method for characterizing the viscoelastic properties of alginate and agarose hydrogel based constructs, which are often used as a model system of soft biological tissues. A sensitive long working distance microscope was used for measuring the time-dependent deformation of the thin circular hydrogel membranes under a constant load. The deformation of the constructs was measured laterally. The elastic modulus as a function of time can be determined by a large deformation theory based on Mooney-Rivlin elasticity. A viscoelastic theory, Zener model, was applied to correlate the time-dependent deformation of the constructs with various gel concentrations, and the creep parameters can therefore be quantitatively estimated. The value of Young's modulus was shown to increase in proportion with gel concentration. This finding is consistent with other publications. Our results also showed the great capability of using the technique to measure gels with incorporated corneal stromal cells. This study demonstrates a novel and convenient technique to measure mechanical properties of hydrogel in a non-destructive, online and realtime fashion. Thus this novel technique can become a valuable tool for soft tissue engineering.