Optimization of a sequential anaerobic-aerobic treatment system to determine ideal reactor sizes for reduction of organic matter (COD) in fishing effluents to legal standards at minimal costs was performed. Calculations for the sequential degradation of effluents for a base case were carried out by an objective function involving process optimization and investment-operation cost related to treatment yield in each reactor. Process optimization considering individual equipment volumes based on biological kinetics gave a minimum total volume for a conversion yield of 0.77 in the anaerobic reactor. The objective function turned out a monotonous decreasing function within the 0-85% conversion yield range of the anaerobic digester. The minimum total cost was found at the superior limit (85%) of the conversion range. Exclusion of the anaerobic step increases by eight times the cost to reach the same level of COD reduction shown by sequential treatment. Experiments at bench scale showed that this system reduces the COD of a base case effluent to 600 mg l(-1), but the final nitrogen content (810 mg l(-1)) remains far above the legal limit (50 mg l(-1)). Parametric sensitivity analysis showed that total annual cost is an increasing exponential function of the COD concentration, an increasing linear function of the energy cost, a decreasing linear function of the COD legal limit and is almost insensitive to oxygen cost. However, aerobic degradation is 27% cheaper by using oxygen instead of aeration. Implementation of the sequential system requires an annual capital investment of US$ 196,000 year(-1) and a discounted operation cost of US$ 138,000 year(-1). The cost of a plant designed to comply with the COD legal limit (160 mg l(-1)) is relatively low as it would only increase the price of fishmeal by 1.0% per tonne.