We develop an original solid respirometric method to measure the biodegradation rates of COD and ammonium at different depths of a Vertical Flow Constructed Wetland (VFCW). The method is developed for a matrix operated under unsaturated conditions. The oxygen demand is measured versus time in a gas passing through a reactor containing a mixture of an organic matrix mixed with a bulking agent (wood). For the measurement of the nitrification rate, a solution of ammonia and hydrogenocarbonates is spread on the sample. We ran 15 experiments on different matrices with variable organic matter contents (sludge, VFCW gravels and sand). Within this paper we present the overall methodology, the factors that allow improving the accuracy (number of duplicates, blank, sample volume, bulking agent volume, gas flow, etc.) and the nitrification rates that were obtained.