In this study, the seasonal and annual changes of key environmental parameters in the Sea of Oman during the period 2005–2012 have been investigated using a range of Earth Observation datasets. Furthermore, the seasonal and spatial variability of those changes to other environmental parameters for the same time period was also explored. Analysis of census of the anti-cyclonic and cyclonic eddies using the Okubo–Waiss algorithm was carried out in a Geographical Information Systems environment using the Marine Geospatial Ecology Tools. Results indicated that the Sea of Oman is mostly influenced by seasonality and by location. The Spearman’s rank correlation test shows a strong, negative correlation between Sea Surface Temperature (SST) and Chlorophyll-a (Chlor-a) in most parts of the sea during the studied period. In terms of spatial variations, eastern parts of the sea showed higher Chlor-a concentrations and lower SST values, especially during summer. The Okubo–Waiss algorithm revealed the existence of 337 eddies, 180 of which are anti-cyclonic eddies with general life span ranging from 4 to 43 weeks, while years 2008 and 2010 presented the most cyclonic eddies. The presence and duration of these eddies proved to be a great contributor in water mixing in the region. Our results clearly demonstrated that this integrated approach improved our understanding of the sea-atmosphere dynamics and environmental variability of the studied region.