This study presents a comparison of two existing methods for the determination of urea concentration in seawater. These methods are referred to here as the enzymatic method, which is based on the use of the enzyme urease, and the direct method, which is based on the reaction of urea with diacetylmonoxime. A room temperature modification of the direct method was adapted for a single reagent and both the enzymatic and the direct method were tested in artificially prepared solutions and in natural samples from estuaries and shelf waters. We were particularly interested in the effects of salinity and humic acids on the accuracy of both methods. The effect of humic acids was negligible. In contrast, salinity ~34 caused a 15% to 40% underestimation in the urea concentrations measured by the enzymatic method and the degree of underestimation varied among enzyme batches. Urea concentrations corrected for the salt effect should, however, be considered estimations, as other factors also interfered with the enzymatic method in natural samples. The direct method as modified in this study presented a low detection limit (0.04 µM urea‐N) and high precision (standard deviation: 0.02 µM urea‐N; coefficient of variation: 1.1%) comparable to those of the enzymatic method. The direct method was more accurate and less salinity dependent than the enzymatic method. As urea levels could have been underestimated by the enzymatic method, our findings support previous conclusions regarding the important role of urea in the nitrogen cycle and its link with some harmful algal bloom phenomena.