Understanding the intricate relationship between fishery resource abundance and environmental factors is paramount for achieving sustainable fishery development and conservation goals. While previous studies have predominantly focused on the direct impacts of environmental factors on stock distribution and resource abundance, the underlying mechanisms remain poorly understood. To address this gap, we investigated the mechanisms through which various environmental factors and their interactions influence the abundance of skipjack tuna populations in Mauritanian waters. Utilizing catch per unit effort (CPUE) data spanning from 2017 to 2019, we employed structural equation modeling (SEM) to construct a comprehensive model assessing the direct and indirect influences of key environmental variables, including sea surface temperature (SST), sea surface salinity (SSS), sea level anomalies (SLA), dissolved oxygen (DO), and chlorophyll-a concentration (Chl-a), on skipjack tuna CPUE. Our findings demonstrate a well-fitting SEM model, revealing direct effects of SST, SSS, SLA, DO, and Chl-a on skipjack tuna CPUE. Notably, DO and SLA exhibited significant positive correlations with CPUE, while SST, SSS, and Chl-a displayed significant negative correlations. Furthermore, environmental factors such as SST exerted indirect effects on skipjack tuna CPUE through multiple pathways, shedding light on the potential impact mechanisms of SST and other environmental variables on skipjack tuna populations in Mauritanian waters.