Continuous remote-sensed daily fields of ocean color now span over two decades; however, it still remains a challenge to examine the ocean ecosystem processes, e.g., phenology, at temporal frequencies of less than a month. This is due to the presence of significantly large gaps in satellite data caused by clouds, sun-glint, and hardware failure; thus, making gap-filling a prerequisite. Commonly used techniques of gap-filling are limited to single value imputation, thus ignoring the error estimates. Though convenient for datasets with fewer missing pixels, these techniques introduce potential biases in datasets having a higher percentage of gaps, such as in the tropical Indian Ocean during the summer monsoon, the satellite coverage is reduced up to 40% due to the seasonally varying cloud cover. In this study, we fill the missing values in the tropical Indian Ocean with a set of plausible values (here, 10,000) using the classical Monte-Carlo method and prepare 10,000 gap-filled datasets of ocean color. Contrary to the previously used gap-filled datasets, the ecological indicators derived using our gap-filled datasets also quantifies uncertainty indicating the likelihood of estimates. Quantification of uncertainty is critical to address the importance of underlying datasets and hence, motivating future observations.