Coastal ecosystems are increasingly exposed to anthropogenic pressures, with oil spills representing a major risk to marine biodiversity. While the impacts of oil spills on macroorganisms have been extensively studied, the response of picoeukaryotes, key primary producers and integral components of marine food webs, remains poorly understood. This study investigates the impact of recurrent oil spills on picoeukaryotic communities by comparing two distinct coastal environments with differing pollution histories. Through integrated chemical analysis, flow cytometry, and 18S rRNA gene sequencing, we evaluated changes in alpha and beta diversity, community composition, and ecological resilience. Our results show that oil spills significantly reduce picoeukaryote abundance and alter community composition, including a marked decline in dominant taxa, such as Ostreococcus. In addition, oil spills appear to enhance community connectivity and interdependence, indicating a shift in ecological interactions under stress. Evidence of recovery dynamics suggests potential resilience following disturbance. These findings highlight the vulnerability of microbial eukaryotes to oil pollution and emphasize the urgent need for improved monitoring and mitigation strategies to preserve the health of coastal ecosystems.