Ocean gateways facilitate circulation between ocean basins, thereby impacting global climate. The Indonesian Gateway transports water from the Pacific to the Indian Ocean via the Indonesian Throughflow (ITF) and drives the strength and intensity of the modern Leeuwin Current, which carries warm equatorial waters along the western coast of Australia to higher latitudes. Therefore, ITF dynamics are a vital component of global thermohaline circulation. Plio-Pleistocene changes in ITF behavior and Leeuwin Current intensity remain poorly constrained due to a lack of sedimentary records from regions under its influence. Here, organic geochemical proxies are used to reconstruct sea surface temperatures on the northwest Australian shelf at IODP Site U1463, downstream of the ITF outlet and under the influence of the Leeuwin Current. Our records, based on TEX 86 and the long-chain diol index, provide insight into past ITF variability (3.5-1.5 Ma) and confirm that sea surface temperature exerted a control on Australian continental hydroclimate. A significant TEX 86 cooling of~5°C occurs within the mid-Pliocene Warm Period (3.3-3.1 Ma) suggesting that this interval was characterized by SST fluctuations at Site U1463. A major feature of both the TEX 86 and long-chain diol index records is a strong cooling from~1.7 to 1.5 Ma. We suggest that this event reflects a reduction in Leeuwin Current intensity due to a major step in ongoing ITF constriction, accompanied by a switch from South to North Pacific source waters entering the ITF inlet. Our new data suggest that an additional ITF constriction event may have occurred in the Pleistocene. Plain Language Summary The Indonesian Throughflow (ITF) represents warm water masses flowing from the western Pacific into the Indian Ocean. The ITF flows through the narrow marine passages of the Indonesian Archipelago. This Indonesian Gateway in turn limits the amount of water moving from the Pacific into the Indian Ocean. The depth and width of the Indonesian Gateway has decreased gradually over the past 5 million years due to tectonic movement, which has caused Indonesian islands such as New Guinea and Halmahera to grow and block water entering the Indonesian Archipelago from the warm South Pacific. As a result, most ITF water now derives from the cooler North Pacific, which impacts Indian Ocean temperatures and broader global ocean circulation and heat distribution. The timing of this shallowing of the Indonesian Gateway and transition from warmer South Pacific to cooler North Pacific ITF source waters is not yet fully understood. Here, we present a new sea surface temperature record from near the ITF outlet that shows intense cooling just after 1.7 million years ago. We suggest that this cooling occurred in response to a significant step in the ongoing tectonic constriction and shallowing of the Indonesian Gateway.