In this study, a 3-step design and optimization method is presented for a bioremediation system utilizing silica gel encapsulated whole-cell biocatalyst. Characterization experiments were conducted to determine the parameters of a steady state reaction/diffusion model for encapsulated AtzA biocatalyst that was subsequently verified experimentally. Dimensionless numbers governing the reaction rate, the Thiele modulus (Phi) and effectiveness factor (eta), were evaluated based on the design parameters of the material, rho (cell loading density) and L-c (characteristic length). Mechanical properties of the gel were determined as a function of rho. Optimal values for rho and L-c were determined for a case study, based on biocatalytic performance, mechanical properties and cost. It was found that free biocatalyst reaction kinetics are first order with K-free = 7.38 x 10(-2) s(-1)/(g cells/mL) and diffusivity of atrazine in the gel increases with rho, from 3.51 x 10(-4) mm(2)/s up to 6.93 x 10(-4) mm(2)/s. Modeling results showed that similar to 20% of activity was lost during encapsulation. Diffusion limitations became significant (Phi > 1) when L-c exceeded 0.1-0.3 mm. The optimal catalyst radius and cell loading density were determined to be L-c = 0.2 mm and rho = 0.11 g cells/mL gel, for an atrazine bioremediation setup with a desired effluent <3 ppb. (C) 2014 Elsevier B.V. All rights reserved.