Time series datasets collected from marine sensors inevitably undergo missing data problems. This cause unreliable sensor data to assist the decision-making process. Many methods are offered to impute missing values. However, selecting the best imputation method is not a trivial task, as it usually requires domain expertise and several trial-and-error iterations. Furthermore, when imputations are carried out in a careless way, it generates a high error factor that can lead stakeholders to wrong assumptions. This paper provides a systematic approach that is able to extract characteristics of underlying data and, based on it, recommends the less error-prone imputation method. We evaluate our proposed method using nine real-world vessel datasets. In total, we generated 3859 data samples consisting of 17 inputs and 1 target feature. Experimental results show that the proposed approach is capable of obtaining a weighted F1-Score of 92.6%. Additionally, when compared with the application of careless selected imputation methods, our work is able to gain up to 86% on the average imputation score, with the worst case gain being of 5%. We empirically demonstrate that the proposed approach is efficient when selecting the best imputation methods.