Nitrification rate as a function of total ammonia nitrogen (TAN) concentration, with and without the interaction of organic matter, was investigated for three types of biofilters of laboratory scale: floating bead filter, fluidized sand filter, and submerged bio-cube filter. The performance of each type of biofilter was evaluated using a 5-reactor series with synthetic solutions containing different carbon/nitrogen ratios (C/N = 0, 0.5, and 2.0). The tests were run at representative cool water aquaculture system temperatures of 15 and 20 °C. The experimental results showed, within the lower total ammonia concentration range, a first-order nitrification rate with a highly linear regression for all three types of biofilters without the interaction of organic carbon at both test temperatures. However, with the addition of organic carbon, the nitrification rate of all three types of biofilters decreased exponentially. The reduction of nitrification rates of the biofilters was about 60–70% for a substrate concentration of 10 mg TAN l⁻¹ when the COD/N ratio increased from 0 to 3. The temperature impact on biofilter nitrification rate was not significant under the two temperatures tested. The results of this study provide useful information for nitrification biofilter design of cool and cold water applications.