The motivation behind our study is to identify a robust method to enhance the accuracy of missing data, particularly chlorophyll-a data, which often goes undetected due to various factors. This study analyzes chlorophyll-a concentrations and sea level changes due to tides using three methods: Linear Interpolation, Fillgaps, and Modified Fillgaps. Two experiments were conducted: Experiment I involved random data removal (60% and 70%), and Experiment II combined sequential and random data removal (25% sequentially on the right, 35% and 45% randomly on the left). In Experiment I, the Modified Fillgaps method showed high correlation coefficients (up to 0.96) between original and reconstructed data, demonstrating its effectiveness in accurately filling significant data gaps. This method also exhibited low Root Mean Square Error and Mean Absolute Error values, confirming its predictive precision. In Experiment II, despite structured and realistic data loss patterns, the method maintained high correlation and low prediction errors, with low Normalized Root Mean Squared Error and Mean Absolute Percentage Error values, further validating its reliability. Additionally, the method excelled in two-dimensional chlorophyll-a maps, outperforming Linear Interpolation and Fillgaps methods in scenarios with 50% and 60% data loss, achieving higher correlation and lower prediction errors. These findings are crucial for environmental and climatological studies relying on satellite-derived data, confirming the Modified Fillgaps method as the most reliable and effective for handling significant data loss in chlorophyll-a map analyses. Future research should explore its application to other environmental data types and more complex data loss patterns.