The Marbled Murrelet (Brachyramphus marmoratus) is a small seabird that is currently listed as threatened in Canada. Understanding this species’ marine habitat preferences plays a vital role in our ability to focus conservation planning. We used the longest-running at-sea survey dataset available in British Columbia to examine hotspot persistence and habitat use at Laskeek Bay, Haida Gwaii, BC. The Laskeek Bay Conservation Society has been conducting spring and summer surveys along fixed transect routes in open and shoreline waters from 1997‒2018. Along with analyzing this long-term dataset, we conducted surveys to measure oceanographic variables (2018–2019) and tested whether murrelets in the same area used prey and oceanographic information to select marine habitat in conjunction with physical habitat features. Our hotspot persistence map, defined as areas that repeatedly had counts above a 75% threshold relative to other areas during a given survey, showed that murrelets consistently preferred shoreline transects. Murrelets also preferred shallow marine areas closer to streams, above higher proportions of sandy substrate and closer proximity to abundant nesting habitat. Modeling weather and time variables contributed little additional predictive power. Nonetheless, models that included physical environmental, oceanographic, and prey variables outperformed those with only physical environmental variables. Stratified water was the oceanographic variable most strongly related to higher counts. Our study suggests that stratified waters could work with stream systems to create productive zones for foraging murrelets, and highlights the importance of murrelets having access to marine areas with the preferred physical features.