Among enhanced oil recovery (EOR) methods, low-salinity waterflooding (LSWF) stands out as a practical and environmentally friendly approach. However, oil-brine incompatibility can cause asphaltene instability, precipitation, and likely formation damage. Due to the lack of published studies at the pore-scale, this work uniquely visualizes asphaltene precipitation during LSWF using a microfluidic technique, allowing real-time observation of oil-brine interactions and damage assessment. Transparent glass micromodels are utilized to simulate oil displacement near the wellbore. Real crude oil samples and various synthetic brines are tested to analyze the effects of asphaltene content and brine salinity on precipitation and deposition pattern. The findings reveal a direct correlation between crude oil asphaltene content and deposition. Lower salinity brines formed stable emulsions, increasing asphaltene deposition in swept zones. In contrast, unswept regions, such as dead-ends, experience lower deposition. This behavior can be attributed to the limited fluid dynamics in unswept regions, where low shear and restricted oil–water contact reduce the formation of emulsions and consequently asphaltene destabilization. Notably, two-times diluted Persian Gulf water (2DSW, ~23,800 ppm) led to 6.8% volumetric precipitation, compared to 5.1% for high-salinity formation brine (FW, ~189,000 ppm). Despite slightly higher deposition with low-salinity brines, the associated salinity change risks—such as plugging, flow impairment, and formation damage due to asphaltene deposition—are negligible under the studied conditions. This is a favorable outcome for deployment of LSWF. Moreover, the study highlights the critical role of brine composition and oil characteristics in LSWF, emphasizing the need for oil-brine compatibility assessment to mitigate any asphaltene-related damage and ensure effective recovery. These insights are essential for optimizing LSWF and minimizing formation damage risks in practical applications.