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The livelihoods of most residents of Tanga (Northern Tanzania) and Malindi (Northern Kenya), rely strongly on fishing activities in the East African shelf region. Thus, understanding variations in sea surface temperature (SST) and its related parameters such as thermocline depths and upper ocean circulation are crucial. This study applies a regional model to understand interannual spatial relationships between ocean circulation and SST off Northern Tanzania and on the Northern Kenya Bank. The results indicate slight differences in variations off the Northern Tanzanian shelf region and the Northern Kenya Bank. Such small variations might have local impacts on the human population through influencing primary productivity and fisheries. The coastal waters off Malindi indicate stronger variations, particularly in 1997 (cold SST) and 1998 (warm SST), than those off Tanga region. The SST anomalies seem to be associated with thermocline and sea surface height (SSH) off Malindi, while off Tanga they relate only to SSH. This information provides further understanding of parameters that may affect fishing activities in these regions and can be used for planning and management processes.